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.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
ants-2.1.0/ANTS.cmake-1-
ants-2.1.0/ANTS.cmake:2:include(${CMAKE_CURRENT_LIST_DIR}/Common.cmake)
ants-2.1.0/ANTS.cmake-3-
##############################################
ants-2.1.0/ANTS.cmake-45-find_package(ITK 4 REQUIRED)
ants-2.1.0/ANTS.cmake:46:include(${ITK_USE_FILE})
ants-2.1.0/ANTS.cmake-47-
##############################################
ants-2.1.0/ANTS.cmake-52- if(VTK_FOUND)
ants-2.1.0/ANTS.cmake:53: include(${VTK_USE_FILE})
ants-2.1.0/ANTS.cmake-54- else(VTK_FOUND)
##############################################
ants-2.1.0/ANTSnightly.sh-10-# make the testing directory, based on current user name
ants-2.1.0/ANTSnightly.sh:11:#user=`who -m | sed -e 's/ .*$//'`
ants-2.1.0/ANTSnightly.sh-12-user=${LOGNAME}
##############################################
ants-2.1.0/ANTSnightly.sh-89-if [ "${OsName}" = "Darwin" ] ; then
ants-2.1.0/ANTSnightly.sh:90: Compiler=clang-`clang -v 2>&1 | head -1 | awk '{print $4}'`
ants-2.1.0/ANTSnightly.sh:91: Compiler=${Compiler}-`clang -v 2>&1 | tail -2 | head -1 | awk '{print $2}'`
ants-2.1.0/ANTSnightly.sh-92- export CC=`which clang`
##############################################
ants-2.1.0/ANTSnightly.sh-133- echo "Building in `pwd`"
ants-2.1.0/ANTSnightly.sh:134: scriptname=`basename $0`
ants-2.1.0/ANTSnightly.sh-135- make -j ${NPROCS}
##############################################
ants-2.1.0/CMake/ExternalData.cmake-607-if(ExternalData_CONFIG)
ants-2.1.0/CMake/ExternalData.cmake:608: include(${ExternalData_CONFIG})
ants-2.1.0/CMake/ExternalData.cmake-609-endif()
##############################################
ants-2.1.0/CMake/ProjectSourceVersion.cmake-37-if(_GIT_VERSION_HASH STREQUAL "GITDIR-NOTFOUND")
ants-2.1.0/CMake/ProjectSourceVersion.cmake:38: include( "${CMAKE_CURRENT_SOURCE_DIR}/CMake/ProjectSourceVersionVars.cmake" )
ants-2.1.0/CMake/ProjectSourceVersion.cmake-39- return()
##############################################
ants-2.1.0/CMake/SlicerMacroCheckExternalProjectDependency.cmake-68- if(EXISTS "${EXTERNAL_PROJECT_DIR}/External_${dep}.cmake")
ants-2.1.0/CMake/SlicerMacroCheckExternalProjectDependency.cmake:69: include(${EXTERNAL_PROJECT_DIR}/External_${dep}.cmake)
ants-2.1.0/CMake/SlicerMacroCheckExternalProjectDependency.cmake-70- elseif(EXISTS "${Slicer_ADDITIONAL_EXTERNAL_PROJECT_DIR}/External_${dep}.cmake")
ants-2.1.0/CMake/SlicerMacroCheckExternalProjectDependency.cmake:71: include(${Slicer_ADDITIONAL_EXTERNAL_PROJECT_DIR}/External_${dep}.cmake)
ants-2.1.0/CMake/SlicerMacroCheckExternalProjectDependency.cmake-72- else()
##############################################
ants-2.1.0/CMake/ANTSExternalData.cmake-1-get_filename_component(_ITKExternalData_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
ants-2.1.0/CMake/ANTSExternalData.cmake:2:include(${_ITKExternalData_DIR}/ExternalData.cmake)
ants-2.1.0/CMake/ANTSExternalData.cmake-3-
##############################################
ants-2.1.0/CMakeLists.txt-51- project(SuperBuild_${LOCAL_PROJECT_NAME})
ants-2.1.0/CMakeLists.txt:52: include("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake")
ants-2.1.0/CMakeLists.txt-53- include(CPack) # This must always be last!
##############################################
ants-2.1.0/CMakeLists.txt-56- project(${LOCAL_PROJECT_NAME})
ants-2.1.0/CMakeLists.txt:57: include("${CMAKE_CURRENT_SOURCE_DIR}/${LOCAL_PROJECT_NAME}.cmake")
ants-2.1.0/CMakeLists.txt-58- include(CPack) # This must always be last!
##############################################
ants-2.1.0/Examples/CMakeLists.txt-175- )
ants-2.1.0/Examples/CMakeLists.txt:176:include(${VTK_USE_FILE})
ants-2.1.0/Examples/CMakeLists.txt-177-include_directories(${VTK_INCLUDE_DIRS})
##############################################
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl.sh-4-ROOT=/home/hwang3/MA2012
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl.sh:5:labels=`cat $ROOT/labels`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl.sh:6:labels1=`cat $ROOT/labels1`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl.sh-7-
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl.sh:8:rates=`cat $ROOT/samplerates1`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl.sh-9-DR=1
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl.sh:10:IDs=`cat $ROOT/Testing/Test`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl.sh:11:TrainIDs=`cat $ROOT/Training/Train`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl.sh-12-
##############################################
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl_qsub.sh-8-
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl_qsub.sh:9:LABELS=`cat $ROOT/labels`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl_qsub.sh-10-L=$1
##############################################
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl_qsub.sh-14-
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl_qsub.sh:15:IDs=`cat $ROOT/Training/Train`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl_qsub.sh-16-
##############################################
ants-2.1.0/ExternalApplications/MALF/CaseStudy/label_fusion.sh-7-lambda=0.1
ants-2.1.0/ExternalApplications/MALF/CaseStudy/label_fusion.sh:8:IDs=`cat $ROOT/Testing/Test`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/label_fusion.sh:9:TrainIDs=`cat $ROOT/Training/Train`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/label_fusion.sh-10-
##############################################
ants-2.1.0/ExternalApplications/MALF/CaseStudy/label_fusion_qsub.sh-13-
ants-2.1.0/ExternalApplications/MALF/CaseStudy/label_fusion_qsub.sh:14:IDs=`cat $ROOT/Training/Train`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/label_fusion_qsub.sh-15-
##############################################
ants-2.1.0/ExternalApplications/MALF/CaseStudy/label_fusion_qsub_train.sh-12-
ants-2.1.0/ExternalApplications/MALF/CaseStudy/label_fusion_qsub_train.sh:13:IDs=`cat $ROOT/Training/Train`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/label_fusion_qsub_train.sh-14-
##############################################
ants-2.1.0/ExternalApplications/MALF/CaseStudy/sa.sh-3-
ants-2.1.0/ExternalApplications/MALF/CaseStudy/sa.sh:4:IDs=`cat $ROOT/Testing/Test`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/sa.sh:5:TrainIDs=`cat $ROOT/Training/Train`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/sa.sh-6-
##############################################
ants-2.1.0/ExternalApplications/MALF/CaseStudy/warpAtlas.sh-3-
ants-2.1.0/ExternalApplications/MALF/CaseStudy/warpAtlas.sh:4:IDs0=`cat $ROOT/Testing/Test`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/warpAtlas.sh:5:IDs=`cat $ROOT/Training/Train`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/warpAtlas.sh-6-
##############################################
ants-2.1.0/ExternalApplications/MALF/CaseStudy/warpAtlas.sh-8- for ref in $IDs0;do
ants-2.1.0/ExternalApplications/MALF/CaseStudy/warpAtlas.sh:9: check=`ls $ROOT/warped/${id}_to_${ref}_image.nii.gz`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/warpAtlas.sh-10- if [[ $check != '' ]]; then
##############################################
ants-2.1.0/ExternalApplications/MALF/CaseStudy/warpAtlas.sh-20- for ref in $IDs;do
ants-2.1.0/ExternalApplications/MALF/CaseStudy/warpAtlas.sh:21: check=`ls $ROOT/warped/${id}_to_${ref}_image.nii.gz`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/warpAtlas.sh-22- if [[ $check != '' ]]; then
##############################################
ants-2.1.0/ProjectSourceVersion.cmake-37-if(_GIT_VERSION_HASH STREQUAL "GITDIR-NOTFOUND")
ants-2.1.0/ProjectSourceVersion.cmake:38: include( "${CMAKE_CURRENT_SOURCE_DIR}/CMake/ProjectSourceVersionVars.cmake" )
ants-2.1.0/ProjectSourceVersion.cmake-39- return()
##############################################
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh-20-PARAM8=0
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:21:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 2 `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:22:for x in $LL ; do PARAM1=` awk -v a=$PARAM1 -v b=$x 'BEGIN{print (a + b)}' ` ; let NFILES=$NFILES+1 ; done
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:23:PARAM1=` awk -v a=$PARAM1 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh-24-
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:25:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 3 `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:26:for x in $LL ; do PARAM2=` awk -v a=$PARAM2 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:27:PARAM2=` awk -v a=$PARAM2 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh-28-
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:29:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 4 `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:30:for x in $LL ; do PARAM3=` awk -v a=$PARAM3 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:31:PARAM3=` awk -v a=$PARAM3 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh-32-
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:33:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 5 `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:34:for x in $LL ; do PARAM4=` awk -v a=$PARAM4 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:35:PARAM4=` awk -v a=$PARAM4 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh-36-
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:37:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 6 `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:38:for x in $LL ; do PARAM5=` awk -v a=$PARAM5 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:39:PARAM5=` awk -v a=$PARAM5 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh-40-
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:41:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 7 `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:42:for x in $LL ; do PARAM6=` awk -v a=$PARAM6 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:43:PARAM6=` awk -v a=$PARAM6 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh-44-
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:45:LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 2 `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:46:for x in $LL ; do PARAM7=` awk -v a=$PARAM7 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:47:PARAM7=` awk -v a=$PARAM7 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh-48-
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:49:LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 3 `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:50:for x in $LL ; do PARAM8=` awk -v a=$PARAM8 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:51:PARAM8=` awk -v a=$PARAM8 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh-52-
##############################################
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-27-PARAM15=0
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:28:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 2 `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:29:for x in $LL ; do PARAM1=` awk -v a=$PARAM1 -v b=$x 'BEGIN{print (a + b)}' ` ; let NFILES=$NFILES+1 ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:30:PARAM1=` awk -v a=$PARAM1 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-31-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:32:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 3 `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:33:for x in $LL ; do PARAM2=` awk -v a=$PARAM2 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:34:PARAM2=` awk -v a=$PARAM2 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-35-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:36:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 4 `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:37:for x in $LL ; do PARAM3=` awk -v a=$PARAM3 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:38:PARAM3=` awk -v a=$PARAM3 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-39-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:40:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 5 `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:41:for x in $LL ; do PARAM4=` awk -v a=$PARAM4 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:42:PARAM4=` awk -v a=$PARAM4 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-43-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:44:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 6 `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:45:for x in $LL ; do PARAM5=` awk -v a=$PARAM5 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:46:PARAM5=` awk -v a=$PARAM5 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-47-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:48:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 7 `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:49:for x in $LL ; do PARAM6=` awk -v a=$PARAM6 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:50:PARAM6=` awk -v a=$PARAM6 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-51-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:52:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 8 `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:53:for x in $LL ; do PARAM7=` awk -v a=$PARAM7 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:54:PARAM7=` awk -v a=$PARAM7 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-55-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:56:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 9 `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:57:for x in $LL ; do PARAM8=` awk -v a=$PARAM8 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:58:PARAM8=` awk -v a=$PARAM8 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-59-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:60:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 10 `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:61:for x in $LL ; do PARAM9=` awk -v a=$PARAM9 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:62:PARAM9=` awk -v a=$PARAM9 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-63-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:64:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 11 `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:65:for x in $LL ; do PARAM10=` awk -v a=$PARAM10 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:66:PARAM10=` awk -v a=$PARAM10 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-67-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:68:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 12 `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:69:for x in $LL ; do PARAM11=` awk -v a=$PARAM11 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:70:PARAM11=` awk -v a=$PARAM11 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-71-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:72:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 13 `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:73:for x in $LL ; do PARAM12=` awk -v a=$PARAM12 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:74:PARAM12=` awk -v a=$PARAM12 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-75-
##############################################
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-78-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:79:LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 2 `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:80:for x in $LL ; do PARAM13=` awk -v a=$PARAM13 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:81:PARAM13=` awk -v a=$PARAM13 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-82-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:83:LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 3 `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:84:for x in $LL ; do PARAM14=` awk -v a=$PARAM14 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:85:PARAM14=` awk -v a=$PARAM14 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-86-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:87:LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 4 `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:88:for x in $LL ; do PARAM15=` awk -v a=$PARAM15 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:89:PARAM15=` awk -v a=$PARAM15 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-90-
##############################################
ants-2.1.0/Scripts/ANTSpexec.sh-9-
ants-2.1.0/Scripts/ANTSpexec.sh:10:`basename $0` [-h] [-r] [-j nb_jobs] command arg_list
ants-2.1.0/Scripts/ANTSpexec.sh-11-
##############################################
ants-2.1.0/Scripts/ANTSpexec.sh-21-
ants-2.1.0/Scripts/ANTSpexec.sh:22: `basename $0` somecommand arg1 arg2 arg3
ants-2.1.0/Scripts/ANTSpexec.sh-23-
ants-2.1.0/Scripts/ANTSpexec.sh:24: `basename $0` -j 3 \"somecommand -r -p\" arg1 arg2 arg3
ants-2.1.0/Scripts/ANTSpexec.sh-25-
ants-2.1.0/Scripts/ANTSpexec.sh:26: `basename $0` -j 6 -r \"convert -scale 50% * small/small_*\" *.jpg"
ants-2.1.0/Scripts/ANTSpexec.sh-27-
##############################################
ants-2.1.0/Scripts/ANTSpexec.sh-42-
ants-2.1.0/Scripts/ANTSpexec.sh:43:`basename $0` [-h] [-r] [-j nb_jobs] command arg_list
ants-2.1.0/Scripts/ANTSpexec.sh-44-
##############################################
ants-2.1.0/Scripts/ANTSpexec.sh-54-
ants-2.1.0/Scripts/ANTSpexec.sh:55: `basename $0` somecommand arg1 arg2 arg3
ants-2.1.0/Scripts/ANTSpexec.sh-56-
ants-2.1.0/Scripts/ANTSpexec.sh:57: `basename $0` -j 3 \"somecommand -r -p\" arg1 arg2 arg3
ants-2.1.0/Scripts/ANTSpexec.sh-58-
ants-2.1.0/Scripts/ANTSpexec.sh:59: `basename $0` -j 6 -r \"convert -scale 50% * small/small_*\" *.jpg"
ants-2.1.0/Scripts/ANTSpexec.sh-60-
##############################################
ants-2.1.0/Scripts/ANTSpexec.sh-112- whm=` whoami `
ants-2.1.0/Scripts/ANTSpexec.sh:113: num=` ps U $whm | grep -i "${PID} " | wc -l `
ants-2.1.0/Scripts/ANTSpexec.sh-114- if [ $num = 2 ] ; then
##############################################
ants-2.1.0/Scripts/ANTSpexec.sh-126- whm=` whoami `
ants-2.1.0/Scripts/ANTSpexec.sh:127: num=` ps U $whm | grep -i "${PID} " | wc -l `
ants-2.1.0/Scripts/ANTSpexec.sh-128- if [ $num = 1 ] ; then
##############################################
ants-2.1.0/Scripts/ANTSpexec.sh-163-
ants-2.1.0/Scripts/ANTSpexec.sh:164:shift `expr $OPTIND - 1` # shift input args, ignore processed args
ants-2.1.0/Scripts/ANTSpexec.sh-165-COMMAND=$1
##############################################
ants-2.1.0/Scripts/ants.sh-66-
ants-2.1.0/Scripts/ants.sh:67:OUTPUTNAME=` echo $MOVING | cut -d '.' -f 1 `
ants-2.1.0/Scripts/ants.sh-68-
##############################################
ants-2.1.0/Scripts/ants.sh-93- TRANSFORMATION=SyN[0.25]
ants-2.1.0/Scripts/ants.sh:94: ITERATLEVEL=(`echo $MAXITERATIONS | tr 'x' ' '`)
ants-2.1.0/Scripts/ants.sh-95- NUMLEVELS=${#ITERATLEVEL[@]}
##############################################
ants-2.1.0/Scripts/antsASLProcessing.sh-17- cat <<USAGE
ants-2.1.0/Scripts/antsASLProcessing.sh:18:`basename $0` performs ASL processing based on ANTs tools. Preprocessing of T1 images using antsCorticalThickness.sh is assumed. The following steps are performed:
ants-2.1.0/Scripts/antsASLProcessing.sh-19- 1) Calculation of average pCASL image.
##############################################
ants-2.1.0/Scripts/antsASLProcessing.sh-27-Required arguments:
ants-2.1.0/Scripts/antsASLProcessing.sh:28:`basename $0` -a anatomical image (skull stripped)
ants-2.1.0/Scripts/antsASLProcessing.sh-29- -p brain segmentation priors (C-style, e.g. priors%d.nii.gz)
##############################################
ants-2.1.0/Scripts/antsASLProcessing.sh-53- cat <<PARAMETERS
ants-2.1.0/Scripts/antsASLProcessing.sh:54: Using `basename $0` with the following parameters:
ants-2.1.0/Scripts/antsASLProcessing.sh-55-
##############################################
ants-2.1.0/Scripts/antsASLProcessing.sh-255-# Do processing.
ants-2.1.0/Scripts/antsASLProcessing.sh:256:if [[ ! -d `dirname $OUTNAME` ]]
ants-2.1.0/Scripts/antsASLProcessing.sh-257-then
ants-2.1.0/Scripts/antsASLProcessing.sh:258: mkdir -p `dirname $OUTNAME`
ants-2.1.0/Scripts/antsASLProcessing.sh-259-fi
##############################################
ants-2.1.0/Scripts/antsAtroposN4.sh-16-
ants-2.1.0/Scripts/antsAtroposN4.sh:17:`basename $0` iterates between N4 <-> Atropos to improve segmentation results.
ants-2.1.0/Scripts/antsAtroposN4.sh-18-
##############################################
ants-2.1.0/Scripts/antsAtroposN4.sh-20-
ants-2.1.0/Scripts/antsAtroposN4.sh:21:`basename $0` -d imageDimension
ants-2.1.0/Scripts/antsAtroposN4.sh-22- -a inputImage
##############################################
ants-2.1.0/Scripts/antsAtroposN4.sh-369-
ants-2.1.0/Scripts/antsAtroposN4.sh:370:echo "--------------------- Running `basename $0` on $HOSTNAME ---------------------"
ants-2.1.0/Scripts/antsAtroposN4.sh-371-
##############################################
ants-2.1.0/Scripts/antsAtroposN4.sh-616-
ants-2.1.0/Scripts/antsAtroposN4.sh:617: `RScript $SEGMENTATION_CONVERGENCE_SCRIPT`
ants-2.1.0/Scripts/antsAtroposN4.sh-618- rm -f $SEGMENTATION_CONVERGENCE_SCRIPT
##############################################
ants-2.1.0/Scripts/antsBrainExtraction.sh-24-
ants-2.1.0/Scripts/antsBrainExtraction.sh:25:`basename $0` performs template-based brain extraction.
ants-2.1.0/Scripts/antsBrainExtraction.sh-26-
##############################################
ants-2.1.0/Scripts/antsBrainExtraction.sh-28-
ants-2.1.0/Scripts/antsBrainExtraction.sh:29:`basename $0` -d imageDimension
ants-2.1.0/Scripts/antsBrainExtraction.sh-30- -a anatomicalImage
##############################################
ants-2.1.0/Scripts/antsBrainExtraction.sh-299-
ants-2.1.0/Scripts/antsBrainExtraction.sh:300:echo "--------------------- Running `basename $0` on $HOSTNAME ---------------------"
ants-2.1.0/Scripts/antsBrainExtraction.sh-301-
##############################################
ants-2.1.0/Scripts/antsCorticalThickness.sh-32-
ants-2.1.0/Scripts/antsCorticalThickness.sh:33:`basename $0` performs T1 anatomical brain processing where the following steps are currently applied:
ants-2.1.0/Scripts/antsCorticalThickness.sh-34-
##############################################
ants-2.1.0/Scripts/antsCorticalThickness.sh-41-
ants-2.1.0/Scripts/antsCorticalThickness.sh:42:`basename $0` -d imageDimension
ants-2.1.0/Scripts/antsCorticalThickness.sh-43- -a anatomicalImage
##############################################
ants-2.1.0/Scripts/antsCorticalThickness.sh-649-
ants-2.1.0/Scripts/antsCorticalThickness.sh:650:echo "--------------------- Running `basename $0` on $HOSTNAME ---------------------"
ants-2.1.0/Scripts/antsCorticalThickness.sh-651-
##############################################
ants-2.1.0/Scripts/antsCorticalThickness.sh-1220-
ants-2.1.0/Scripts/antsCorticalThickness.sh:1221:ccmetric=`${ANTSPATH}/ImageMath ${DIMENSION} a PearsonCorrelation ${REGISTRATION_TEMPLATE} ${EXTRACTED_SEGMENTATION_BRAIN_DEFORMED} ${REGISTRATION_TEMPLATE_BRAIN_MASK}`
ants-2.1.0/Scripts/antsCorticalThickness.sh:1222:bvol=`${ANTSPATH}/ImageMath ${DIMENSION} a total ${BRAIN_EXTRACTION_MASK} | cut -d ':' -f 2 | cut -d ' ' -f 2 `
ants-2.1.0/Scripts/antsCorticalThickness.sh:1223:gvol=`${ANTSPATH}/ImageMath ${DIMENSION} a total ${BRAIN_SEGMENTATION_GM} | cut -d ':' -f 2 | cut -d ' ' -f 2 `
ants-2.1.0/Scripts/antsCorticalThickness.sh:1224:wvol=`${ANTSPATH}/ImageMath ${DIMENSION} a total ${BRAIN_SEGMENTATION_WM} | cut -d ':' -f 2 | cut -d ' ' -f 2 `
ants-2.1.0/Scripts/antsCorticalThickness.sh:1225:thks=`${ANTSPATH}/ImageMath ${DIMENSION} a total $CORTICAL_THICKNESS_IMAGE | cut -d ':' -f 2 | cut -d ' ' -f 2 `
ants-2.1.0/Scripts/antsCorticalThickness.sh-1226-echo "PearsonCorrelation,BVOL,GVol,WVol,ThicknessSum" > ${OUTPUT_PREFIX}brainvols.csv
##############################################
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh-16-
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh:17:`basename $0` performs restration between a scalar image and a T1 image:
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh-18-
##############################################
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh-20-
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh:21:`basename $0` -d imageDimension
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh-22- -r anatomicalT1image (brain or whole-head, depending on modality) to align to
##############################################
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh-260-
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh:261:echo "--------------------- Running `basename $0` on $HOSTNAME ---------------------"
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh-262-
##############################################
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh-317- # FIXME - how to name these reasonably
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh:318: AUXO=`basename ${AUX_IMAGES[$i]} .nii.gz`
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh-319- #AUXO=${OUTPUT_PREFIX}_aux_${i}_warped.nii.gz
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-21-
ants-2.1.0/Scripts/antsIntroduction.sh:22:Alternatively, edit this script ( `basename $0` ) to set up this parameter correctly.
ants-2.1.0/Scripts/antsIntroduction.sh-23-
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-46-
ants-2.1.0/Scripts/antsIntroduction.sh:47:`basename $0` -d ImageDimension -r fixed.ext -i moving.ext
ants-2.1.0/Scripts/antsIntroduction.sh-48-
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-76-
ants-2.1.0/Scripts/antsIntroduction.sh:77: Use `basename $0` -h for extended help.
ants-2.1.0/Scripts/antsIntroduction.sh-78---------------------------------------------------------------------------------------
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-93-
ants-2.1.0/Scripts/antsIntroduction.sh:94: `basename $0` will perform an elastic or diffeomorphic transformation of the moving image
ants-2.1.0/Scripts/antsIntroduction.sh-95- into the fixed image space.
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-103-
ants-2.1.0/Scripts/antsIntroduction.sh:104: `basename $0` -d ImageDimension -r fixed.ext -i moving.ext
ants-2.1.0/Scripts/antsIntroduction.sh-105-
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-288-# put all related processes in array
ants-2.1.0/Scripts/antsIntroduction.sh:289: runningANTSpids=( `ps -C ANTS -C N4BiasFieldCorrection -C antsIntroduction.sh | awk '{ printf "%s\n", $1 ; }'` )
ants-2.1.0/Scripts/antsIntroduction.sh-290-
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-349- MOVING=$OPTARG
ants-2.1.0/Scripts/antsIntroduction.sh:350: OUTPUTNAME=` echo basename $MOVING | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsIntroduction.sh-351- ;;
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-391-
ants-2.1.0/Scripts/antsIntroduction.sh:392:FIXED=`basename ${FIXED}`
ants-2.1.0/Scripts/antsIntroduction.sh:393:MOVING=`basename ${MOVING}`
ants-2.1.0/Scripts/antsIntroduction.sh-394-
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-415-echo "input files: checking"
ants-2.1.0/Scripts/antsIntroduction.sh:416:compareheaders=`${ANTSPATH}/ImageMath $DIM ${OUTPUTNAME}repaired.nii.gz CompareHeadersAndImages $FIXED $MOVING | grep FailureState | cut -d ' ' -f 4 `
ants-2.1.0/Scripts/antsIntroduction.sh-417-
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-426-
ants-2.1.0/Scripts/antsIntroduction.sh:427:ITERATLEVEL=(`echo $MAXITERATIONS | tr 'x' ' '`)
ants-2.1.0/Scripts/antsIntroduction.sh-428-NUMLEVELS=${#ITERATLEVEL[@]}
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-504-else
ants-2.1.0/Scripts/antsIntroduction.sh:505:echo "Invalid transformation metric. Use RI, RA, EL, SY, S2, GR , DD or EX or type bash `basename $0` -h."
ants-2.1.0/Scripts/antsIntroduction.sh-506-exit 1
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-534-else
ants-2.1.0/Scripts/antsIntroduction.sh:535:echo "Invalid similarity metric. Use CC, MI, MSQ or PR or type bash`basename $0` -h."
ants-2.1.0/Scripts/antsIntroduction.sh-536-exit 1
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-542-
ants-2.1.0/Scripts/antsIntroduction.sh:543:MOVINGBASE=` echo ${MOVING} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsIntroduction.sh-544-
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-602-echo "--------------------------------------------------------------------------------------"
ants-2.1.0/Scripts/antsIntroduction.sh:603:FIXEDBASE=` echo ${FIXED} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsIntroduction.sh-604-${ANTSPATH}/WarpImageMultiTransform $DIM ${FIXED} ${FIXEDBASE}_InverseWarp.nii.gz -R ${MOVING} -i ${OUTPUTNAME}Affine.txt ${OUTPUTNAME}InverseWarp.nii.gz
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-651-echo "--------------------------------------------------------------------------------------"
ants-2.1.0/Scripts/antsIntroduction.sh:652:FIXEDBASE=` echo ${FIXED} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsIntroduction.sh-653-${ANTSPATH}/WarpImageMultiTransform $DIM ${FIXED} ${FIXEDBASE}_InverseWarp.nii.gz -i ${OUTPUTNAME}Affine.txt ${OUTPUTNAME}InverseWarp.nii.gz -R ${OUTPUTNAME}.nii.gz
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-739-# save output in starting dir - remove inputs, then remove tempdir
ants-2.1.0/Scripts/antsIntroduction.sh:740:rm `basename ${FIXED}`
ants-2.1.0/Scripts/antsIntroduction.sh:741:rm `basename ${MOVING}`
ants-2.1.0/Scripts/antsIntroduction.sh-742-cp * ../
##############################################
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh-32-
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh:33:`basename $0` performs a longitudinal cortical thickness estimation. The following steps
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh-34-are performed:
##############################################
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh-47-
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh:48:`basename $0` -d imageDimension
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh-49- -e brainTemplate
##############################################
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh-537-
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh:538:echo "--------------------- Running `basename $0` on $HOSTNAME ---------------------"
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh-539-
##############################################
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh-854-
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh:855: BASENAME_ID=`basename ${ANATOMICAL_IMAGES[$i]}`
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh-856- BASENAME_ID=${BASENAME_ID/\.nii\.gz/}
##############################################
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh-888- do
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh:889: BASENAME_LOCAL_ID=`basename ${ANATOMICAL_IMAGES[$j]}`
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh-890- BASENAME_LOCAL_ID=${BASENAME_LOCAL_ID/\.nii\.gz/}
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-21-
ants-2.1.0/Scripts/antsMalfLabeling.sh:22:Alternatively, edit this script ( `basename $0` ) to set up this parameter correctly.
ants-2.1.0/Scripts/antsMalfLabeling.sh-23-
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-74-
ants-2.1.0/Scripts/antsMalfLabeling.sh:75:`basename $0` -d ImageDimension -o OutputPrefix <other options> <images>
ants-2.1.0/Scripts/antsMalfLabeling.sh-76-
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-112-
ants-2.1.0/Scripts/antsMalfLabeling.sh:113:`basename $0` -d 3 -t target.nii.gz -o malf \
ants-2.1.0/Scripts/antsMalfLabeling.sh-114- -p malfPosteriors%04d.nii.gz \
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-142-
ants-2.1.0/Scripts/antsMalfLabeling.sh:143:`basename $0` will propagate labels from a set of pre-labeled atlases using the MALF
ants-2.1.0/Scripts/antsMalfLabeling.sh-144-algorithm.
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-147-
ants-2.1.0/Scripts/antsMalfLabeling.sh:148:`basename $0` -d ImageDimension -o OutputPrefix <other options> <images>
ants-2.1.0/Scripts/antsMalfLabeling.sh-149-
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-151-
ants-2.1.0/Scripts/antsMalfLabeling.sh:152:`basename $0` -d 3 -t target.nii.gz -o malf \
ants-2.1.0/Scripts/antsMalfLabeling.sh-153- -p malfPosteriors%04d.nii.gz \
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-262-# put all related processes in array
ants-2.1.0/Scripts/antsMalfLabeling.sh:263:runningANTSpids=( `ps -C antsRegistration -C ImageMath| awk '{ printf "%s\n", $1 ; }'` )
ants-2.1.0/Scripts/antsMalfLabeling.sh-264-
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-310-##Getting system info from linux can be done with these variables.
ants-2.1.0/Scripts/antsMalfLabeling.sh:311:# RAM=`cat /proc/meminfo | sed -n -e '/MemTotal/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
ants-2.1.0/Scripts/antsMalfLabeling.sh:312:# RAMfree=`cat /proc/meminfo | sed -n -e '/MemFree/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
ants-2.1.0/Scripts/antsMalfLabeling.sh-313-# cpu_free_ram=$((${RAMfree}/${cpu_count}))
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-378- OUTPUT_PREFIX=$OPTARG
ants-2.1.0/Scripts/antsMalfLabeling.sh:379: OUTPUT_DIR=`dirname ${OUTPUT_PREFIX}`
ants-2.1.0/Scripts/antsMalfLabeling.sh-380- ;;
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-450- do
ants-2.1.0/Scripts/antsMalfLabeling.sh:451: IMG_BASE=`basename ${ATLAS_IMAGES[$i]}`
ants-2.1.0/Scripts/antsMalfLabeling.sh:452: BASENAME=` echo ${IMG_BASE} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsMalfLabeling.sh-453-
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-497- then
ants-2.1.0/Scripts/antsMalfLabeling.sh:498: id=`qsub -cwd -S /bin/bash -N antsMalfReg -v ANTSPATH=$ANTSPATH $QSUB_OPTS $qscript | awk '{print $3}'`
ants-2.1.0/Scripts/antsMalfLabeling.sh-499- jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-502- then
ants-2.1.0/Scripts/antsMalfLabeling.sh:503: id=`qsub -N antsMalfReg -v ANTSPATH=$ANTSPATH $QSUB_OPTS -q nopreempt -l nodes=1:ppn=1 -l mem=8gb -l walltime=20:00:00 $qscript | awk '{print $1}'`
ants-2.1.0/Scripts/antsMalfLabeling.sh-504- jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-507- then
ants-2.1.0/Scripts/antsMalfLabeling.sh:508: id=`xgrid $XGRID_OPTS -job submit /bin/bash $qscript | awk '{sub(/;/,"");print $3}' | tr '\n' ' ' | sed 's: *: :g'`
ants-2.1.0/Scripts/antsMalfLabeling.sh-509- jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-552-
ants-2.1.0/Scripts/antsMalfLabeling.sh:553: OVERLAP_MEASURES=( `${ANTSPATH}/LabelOverlapMeasures ${DIM} ${TMP_WARPED_ATLAS_LABEL_MASK} ${TARGET_MASK_IMAGE} 1` )
ants-2.1.0/Scripts/antsMalfLabeling.sh-554- TOKENS=( ${OVERLAP_MEASURES[1]//,/\ } )
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-624-
ants-2.1.0/Scripts/antsMalfLabeling.sh:625: OVERLAP_MEASURES=( `${ANTSPATH}/LabelOverlapMeasures ${DIM} ${TMP_WARPED_ATLAS_LABEL_MASK} ${TARGET_MASK_IMAGE} 1` )
ants-2.1.0/Scripts/antsMalfLabeling.sh-626- TOKENS=( ${OVERLAP_MEASURES[1]//,/\ } )
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-664-
ants-2.1.0/Scripts/antsMalfLabeling.sh:665: jobIDs=`qsub -cwd -S /bin/bash -N antsMalf -v ANTSPATH=$ANTSPATH $QSUB_OPTS $qscript2 | awk '{print $3}'`
ants-2.1.0/Scripts/antsMalfLabeling.sh-666- ${ANTSPATH}/waitForSGEQJobs.pl 1 600 $jobIDs
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-695-
ants-2.1.0/Scripts/antsMalfLabeling.sh:696: OVERLAP_MEASURES=( `${ANTSPATH}/LabelOverlapMeasures ${DIM} ${TMP_WARPED_ATLAS_LABEL_MASK} ${TARGET_MASK_IMAGE} 1` )
ants-2.1.0/Scripts/antsMalfLabeling.sh-697- TOKENS=( ${OVERLAP_MEASURES[1]//,/\ } )
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-735-
ants-2.1.0/Scripts/antsMalfLabeling.sh:736: jobIDs=`qsub -N antsMalf -v ANTSPATH=$ANTSPATH $QSUB_OPTS -q nopreempt -l nodes=1:ppn=1 -l mem=8gb -l walltime=30:00:00 $qscript2 | awk '{print $1}'`
ants-2.1.0/Scripts/antsMalfLabeling.sh-737- ${ANTSPATH}/waitForPBSQJobs.pl 1 600 $jobIDs
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-754-
ants-2.1.0/Scripts/antsMalfLabeling.sh:755: OVERLAP_MEASURES=( `${ANTSPATH}/LabelOverlapMeasures ${DIM} ${TMP_WARPED_ATLAS_LABEL_MASK} ${TARGET_MASK_IMAGE} 1` )
ants-2.1.0/Scripts/antsMalfLabeling.sh-756- TOKENS=( ${OVERLAP_MEASURES[1]//,/\ } )
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-824-
ants-2.1.0/Scripts/antsMalfLabeling.sh:825: OVERLAP_MEASURES=( `${ANTSPATH}/LabelOverlapMeasures ${DIM} ${TMP_WARPED_ATLAS_LABEL_MASK} ${TARGET_MASK_IMAGE} 1` )
ants-2.1.0/Scripts/antsMalfLabeling.sh-826- TOKENS=( ${OVERLAP_MEASURES[1]//,/\ } )
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-21-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:22:Alternatively, edit this script ( `basename $0` ) to set up this parameter correctly.
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-23-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-70-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:71:`basename $0` -d ImageDimension -o OUTPREFIX <other options> <images>
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-72-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-130-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:131:`basename $0` -d 3 -m 30x50x20 -t GR -s CC -c 1 -o MY -z InitialTemplate.nii.gz *RF*T1x.nii.gz
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-132-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-227- echo " shapeupdatetotemplate---voxel-wise averaging of the inverse warp fields (from subject to template)"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:228: echo " ${ANTSPATH}/AverageImages $dim ${templatename}${whichtemplate}warp.nii.gz 0 `ls ${outputname}*Warp.nii.gz | grep -v "InverseWarp"`"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-229- echo "--------------------------------------------------------------------------------------"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-230-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:231: ${ANTSPATH}/AverageImages $dim ${templatename}${whichtemplate}warp.nii.gz 0 `ls ${outputname}*Warp.nii.gz | grep -v "InverseWarp"`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-232-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-263-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:264: outdir=`dirname ${TEMPLATES[0]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-265- if [[ ${#outdir} -eq 0 ]]
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-269-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:270: files=`ls ${outdir}/job*.sh`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:271: BASENAME1=`echo $files[1] | cut -d 'b' -f 1`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-272-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-277- then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:278: BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-279- mv "$file" "${BASENAME1}b_000${BASENAME2}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-282- then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:283: BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-284- mv "$file" "${BASENAME1}b_00${BASENAME2}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-287- then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:288: BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-289- mv "$file" "${BASENAME1}b_0${BASENAME2}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-317-# put all related processes in array
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:318: runningANTSpids=( `ps -C ANTS -C N4BiasFieldCorrection -C ImageMath| awk '{ printf "%s\n", $1 ; }'` )
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-319-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-380-##Getting system info from linux can be done with these variables.
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:381:# RAM=`cat /proc/meminfo | sed -n -e '/MemTotal/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:382:# RAMfree=`cat /proc/meminfo | sed -n -e '/MemFree/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-383-# cpu_free_ram=$((${RAMfree}/${cpu_count}))
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-537-else
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:538: MODALITYWEIGHTS=(`echo $MODALITYWEIGHTSTRING | tr 'x' "\n"`)
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-539- if [[ ${#MODALITYWEIGHTS[@]} -ne $NUMBEROFMODALITIES ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-574- echo "Please provide at least 2 filenames for the template."
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:575: echo "Use `basename $0` -h for help"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-576- exit 1
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-578- then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:579: extension=`echo ${IMAGESETVARIABLE#*.}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-580- if [[ $extension = 'csv' || $extension = 'txt' ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-585- do
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:586: files=(`echo $line | tr ',' ' '`)
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-587- if [[ ${#files[@]} -ne $NUMBEROFMODALITIES ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-599- else
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:600: range=`${ANTSPATH}/ImageMath $TDIM abs nvols ${IMAGESETVARIABLE} | tail -1 | cut -d "," -f 4 | cut -d " " -f 2 | cut -d "]" -f 1 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-601- if [[ ${range} -eq 1 && ${TDIM} -ne 4 ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-603- echo "Please provide at least 2 filenames for the template."
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:604: echo "Use `basename $0` -h for help"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-605- exit 1
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-608- echo "This is a multivolume file. Use -d 4"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:609: echo "Use `basename $0` -h for help"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-610- exit 1
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-769-# remove old job bash scripts
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:770:outdir=`dirname ${TEMPLATES[0]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-771-if [[ ${#outdir} -eq 0 ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-798-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:799: IMGbase=`basename ${IMAGESETARRAY[$i]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:800: BASENAME=` echo ${IMGbase} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-801- RIGID="${outdir}/rigid${i}_0_${IMGbase}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-813- let k=$i+$j
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:814: IMGbase=`basename ${IMAGESETARRAY[$k]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:815: BASENAME=` echo ${IMGbase} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-816- RIGID="${outdir}/rigid${i}_${j}_${IMGbase}"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:817: IMGbaseBASE=`basename ${IMAGESETARRAY[$i]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:818: BASENAMEBASE=` echo ${IMGbaseBASE} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-819- exe2="$exe2 ${WARP} $DIM ${IMAGESETARRAY[$k]} $RIGID ${outdir}/rigid${i}_0_${BASENAMEBASE}Affine.txt -R ${TEMPLATES[$j]}\n"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-826- then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:827: id=`qsub -cwd -S /bin/bash -N antsBuildTemplate_rigid -v ANTSPATH=$ANTSPATH $QSUBOPTS $qscript | awk '{print $3}'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-828- jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-831- then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:832: id=`qsub -N antsrigid -v ANTSPATH=$ANTSPATH $QSUBOPTS -q nopreempt -l nodes=1:ppn=1 -l walltime=20:00:00 -l mem=8gb $qscript | awk '{print $1}'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-833- jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-841- then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:842: id=`xgrid $XGRIDOPTS -job submit /bin/bash $qscript | awk '{sub(/;/,"");print $3}' | tr '\n' ' ' | sed 's: *: :g'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-843- #echo "xgrid $XGRIDOPTS -job submit /bin/bash $qscript"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-919- let k=$i-$j
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:920: IMGbase=`basename ${IMAGESETARRAY[$i]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:921: BASENAME=` echo ${IMGbase} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-922- RIGID="${outdir}/rigid${k}_${j}_${IMGbase}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-971-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:972:ITERATLEVEL=(` echo $MAXITERATIONS | tr 'x' ' ' `)
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-973-NUMLEVELS=${#ITERATLEVEL[@]}
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1045-else
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1046: echo "Invalid transformation metric. Use EL, SY, S2, GR , DD or EX or type bash `basename $0` -h."
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1047- exit 1
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1114- else
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1115: echo "Invalid similarity metric. Use CC, MI, MSQ or PR or type bash `basename $0` -h."
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1116- exit 1
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1117- fi
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1118: TEMPLATEbase=`basename ${TEMPLATES[$k]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1119: indir=`dirname ${IMAGESETARRAY[$j]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1120- if [[ ${#indir} -eq 0 ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1123- fi
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1124: IMGbase=`basename ${IMAGESETARRAY[$l]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1125- POO=${OUTPUTNAME}template${k}${IMGbase}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1126- OUTFN=${POO%.*.*}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1127: OUTFN=`basename ${OUTFN}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1128- DEFORMED="${outdir}/${OUTFN}${l}WarpedToTemplate.nii.gz"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1129-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1130: IMGbase=`basename ${IMAGESETARRAY[$j]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1131- POO=${OUTPUTNAME}${IMGbase}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1132- OUTWARPFN=${POO%.*.*}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1133: OUTWARPFN=`basename ${OUTWARPFN}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1134- OUTWARPFN="${OUTWARPFN}${j}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1151-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1152: IMGbase=`basename ${IMAGESETARRAY[$j]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1153- POO=${OUTPUTNAME}${IMGbase}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1154- OUTWARPFN=${POO%.*.*}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1155: OUTWARPFN=`basename ${OUTWARPFN}${j}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1156-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1171- echo -e "$exe" > $qscript
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1172: id=`qsub -cwd -N antsBuildTemplate_deformable_${i} -S /bin/bash -v ANTSPATH=$ANTSPATH $QSUBOPTS $qscript | awk '{print $3}'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1173- jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1178- echo -e "$exe" >> $qscript
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1179: id=`qsub -N antsdef${i} -v ANTSPATH=$ANTSPATH -q nopreempt -l nodes=1:ppn=1 -l walltime=20:00:00 -l mem=8gb $QSUBOPTS $qscript | awk '{print $1}'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1180- jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1188- echo -e "$exe" >> $qscript
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1189: id=`xgrid $XGRIDOPTS -job submit /bin/bash $qscript | awk '{sub(/;/,"");print $3}' | tr '\n' ' ' | sed 's: *: :g'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1190- jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1197- # counter updated, but not directly used in this loop
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1198: count=`expr $count + 1`;
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1199- # echo " submitting job number $count " # for debugging only
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-21-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:22:Alternatively, edit this script ( `basename $0` ) to set up this parameter correctly.
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-23-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-70-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:71:`basename $0` -d ImageDimension -o OutputPrefix <other options> <images>
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-72-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-182-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:183:`basename $0` -d 3 -i 3 -k 1 -f 4x2x1 -s 2x1x0vox -q 30x20x4 -t SyN -m CC -c 0 -o MY sub*avg.nii.gz
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-184-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-301-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:302: imagelist=(`ls ${outputname}template${whichtemplate}*WarpedToTemplate.nii.gz`)
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-303- if [[ ${#imagelist[@]} -eq 0 ]] ; then
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-309-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:310: WARPLIST=( `ls ${outputname}*[0-9]Warp.nii.gz 2> /dev/null` )
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-311- NWARPS=${#WARPLIST[*]}
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-322- echo " shapeupdatetotemplate---voxel-wise averaging of the inverse warp fields (from subject to template)"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:323: echo " ${ANTSPATH}/AverageImages $dim ${templatename}${whichtemplate}warp.nii.gz 0 `ls ${outputname}*Warp.nii.gz | grep -v "InverseWarp"`"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-324- date
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-325- echo "--------------------------------------------------------------------------------------"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:326: ${ANTSPATH}/AverageImages $dim ${templatename}${whichtemplate}warp.nii.gz 0 `ls ${outputname}*Warp.nii.gz | grep -v "InverseWarp"`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-327-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-369-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:370: outdir=`dirname ${TEMPLATES[0]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-371- if [[ ${#outdir} -eq 0 ]]
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-375-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:376: files=`ls ${outdir}/job*.sh`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:377: BASENAME1=`echo $files[1] | cut -d 'b' -f 1`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-378-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-383- then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:384: BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-385- mv "$file" "${BASENAME1}b_000${BASENAME2}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-388- then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:389: BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-390- mv "$file" "${BASENAME1}b_00${BASENAME2}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-393- then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:394: BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-395- mv "$file" "${BASENAME1}b_0${BASENAME2}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-423-# put all related processes in array
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:424:runningANTSpids=( `ps -C antsRegistration -C N4BiasFieldCorrection -C ImageMath| awk '{ printf "%s\n", $1 ; }'` )
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-425-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-486-##Getting system info from linux can be done with these variables.
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:487:# RAM=`cat /proc/meminfo | sed -n -e '/MemTotal/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:488:# RAMfree=`cat /proc/meminfo | sed -n -e '/MemFree/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-489-# cpu_free_ram=$((${RAMfree}/${cpu_count}))
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-665- else
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:666: MODALITYWEIGHTS=(`echo $MODALITYWEIGHTSTRING | tr 'x' "\n"`)
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-667- if [[ ${#MODALITYWEIGHTS[@]} -ne $NUMBEROFMODALITIES ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-719-else
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:720: echo "Invalid transformation. See `basename $0` -h for help menu."
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-721- exit 1
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-752- echo "Please provide at least 2 filenames for the template inputs."
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:753: echo "Use `basename $0` -h for help"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-754- exit 1
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-756- then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:757: extension=`echo ${IMAGESETVARIABLE#*.}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-758- if [[ $extension = 'csv' || $extension = 'txt' ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-763- do
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:764: files=(`echo $line | tr ',' ' '`)
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-765- if [[ ${#files[@]} -ne $NUMBEROFMODALITIES ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-777- else
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:778: range=`${ANTSPATH}/ImageMath $TDIM abs nvols ${IMAGESETVARIABLE} | tail -1 | cut -d "," -f 4 | cut -d " " -f 2 | cut -d "]" -f 1 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-779- if [[ ${range} -eq 1 && ${TDIM} -ne 4 ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-781- echo "Please provide at least 2 filenames for the template."
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:782: echo "Use `basename $0` -h for help"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-783- exit 1
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-786- echo "This is a multivolume file. Use -d 4"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:787: echo "Use `basename $0` -h for help"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-788- exit 1
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-949-# remove old job bash scripts
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:950:outdir=`dirname ${TEMPLATES[0]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-951-if [[ ${#outdir} -eq 0 ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-986-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:987: IMGbase=`basename ${IMAGESETARRAY[$i]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:988: BASENAME=` echo ${IMGbase} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-989- RIGID="${outdir}/rigid${i}_0_${IMGbase}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-999- let k=$i+$j
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1000: IMGbase=`basename ${IMAGESETARRAY[$k]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1001: BASENAME=` echo ${IMGbase} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1002- RIGID="${outdir}/rigid${i}_${j}_${IMGbase}"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1003: IMGbaseBASE=`basename ${IMAGESETARRAY[$i]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1004: BASENAMEBASE=` echo ${IMGbaseBASE} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1005- exe2="$exe2 ${WARP} -d $DIM --float $USEFLOAT -i ${IMAGESETARRAY[$k]} -o $RIGID -t ${outdir}/rigid${i}_0GenericAffine.mat -r ${TEMPLATES[$j]}\n"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1012- then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1013: id=`qsub -cwd -S /bin/bash -N antsBuildTemplate_rigid -v ANTSPATH=$ANTSPATH $QSUBOPTS $qscript | awk '{print $3}'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1014- jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1017- then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1018: id=`qsub -N antsrigid -v ANTSPATH=$ANTSPATH $QSUBOPTS -q nopreempt -l nodes=1:ppn=1 -l mem=${PBSMEMORY} -l walltime=${PBSWALLTIME} $qscript | awk '{print $1}'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1019- jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1027- then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1028: id=`xgrid $XGRIDOPTS -job submit /bin/bash $qscript | awk '{sub(/;/,"");print $3}' | tr '\n' ' ' | sed 's: *: :g'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1029- #echo "xgrid $XGRIDOPTS -job submit /bin/bash $qscript"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1106- let k=$i-$j
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1107: IMGbase=`basename ${IMAGESETARRAY[$i]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1108: BASENAME=` echo ${IMGbase} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1109- RIGID="${outdir}/rigid${k}_${j}_${IMGbase}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1156-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1157:ITERATLEVEL=(` echo $MAXITERATIONS | tr 'x' ' ' `)
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1158-NUMLEVELS=${#ITERATLEVEL[@]}
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1244- else
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1245: echo "Invalid similarity metric. Use CC, MI, MSQ, DEMONS or type bash `basename $0` -h."
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1246- exit 1
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1247- fi
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1248: TEMPLATEbase=`basename ${TEMPLATES[$k]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1249: indir=`dirname ${IMAGESETARRAY[$j]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1250- if [[ ${#indir} -eq 0 ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1253- fi
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1254: IMGbase=`basename ${IMAGESETARRAY[$l]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1255- POO=${OUTPUTNAME}template${k}${IMGbase}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1256- OUTFN=${POO%.*.*}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1257: OUTFN=`basename ${OUTFN}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1258- DEFORMED="${outdir}/${OUTFN}${l}WarpedToTemplate.nii.gz"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1259-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1260: IMGbase=`basename ${IMAGESETARRAY[$j]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1261- POO=${OUTPUTNAME}${IMGbase}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1262- OUTWARPFN=${POO%.*.*}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1263: OUTWARPFN=`basename ${OUTWARPFN}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1264- OUTWARPFN="${OUTWARPFN}${j}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1293-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1294: IMGbase=`basename ${IMAGESETARRAY[$j]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1295- POO=${OUTPUTNAME}${IMGbase}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1296- OUTWARPFN=${POO%.*.*}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1297: OUTWARPFN=`basename ${OUTWARPFN}${j}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1298-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1333- echo -e "$exe" > $qscript
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1334: id=`qsub -cwd -N antsBuildTemplate_deformable_${i} -S /bin/bash -v ANTSPATH=$ANTSPATH $QSUBOPTS $qscript | awk '{print $3}'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1335- jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1340- echo -e "$exe" >> $qscript
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1341: id=`qsub -N antsdef${i} -v ANTSPATH=$ANTSPATH -q nopreempt -l nodes=1:ppn=1 -l mem=${PBSMEMORY} -l walltime=${PBSWALLTIME} $QSUBOPTS $qscript | awk '{print $1}'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1342- jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1350- echo -e "$exe" >> $qscript
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1351: id=`xgrid $XGRIDOPTS -job submit /bin/bash $qscript | awk '{sub(/;/,"");print $3}' | tr '\n' ' ' | sed 's: *: :g'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1352- jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1359- # counter updated, but not directly used in this loop
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1360: count=`expr $count + 1`;
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1361- # echo " submitting job number $count " # for debugging only
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1420-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1421: WARPFILES=`ls ${OUTPUTNAME}*Warp.nii.gz | grep -v "InverseWarp"`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1422: AFFINEFILES=`ls ${OUTPUTNAME}*GenericAffine.mat`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1423-
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-218- if ( ! -d "${outdir}${dirname}") {
ants-2.1.0/Scripts/antsNeuroimagingBattery:219: `mkdir -p ${outdir}${dirname}`;
ants-2.1.0/Scripts/antsNeuroimagingBattery-220- }
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-223- my $ref = "${obase}ref.nii.gz";
ants-2.1.0/Scripts/antsNeuroimagingBattery:224: system("${ANTSPATH}/ImageMath 3 $ref m $anat $mask" );
ants-2.1.0/Scripts/antsNeuroimagingBattery-225- my $res = "${ANTSPATH}/ResampleImageBySpacing 3 $ref $ref 2.0 2.0 2.0";
ants-2.1.0/Scripts/antsNeuroimagingBattery-226- print("$res\n");
ants-2.1.0/Scripts/antsNeuroimagingBattery:227: system($res);
ants-2.1.0/Scripts/antsNeuroimagingBattery-228-
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-230- print( "$dtiexe\n");
ants-2.1.0/Scripts/antsNeuroimagingBattery:231: system( $dtiexe );
ants-2.1.0/Scripts/antsNeuroimagingBattery-232-
ants-2.1.0/Scripts/antsNeuroimagingBattery:233: system("${ANTSPATH}/ImageMath 3 ${outdir}${dirname}${outname}${outid}fa_anatomical.nii.gz TensorFA ${outdir}${dirname}${outname}${outid}dt_anatomical.nii.gz");
ants-2.1.0/Scripts/antsNeuroimagingBattery:234: system("${ANTSPATH}/ImageMath 3 ${outdir}${dirname}${outname}${outid}fa_anatomical.nii.gz m ${outdir}${dirname}${outname}${outid}fa_anatomical.nii.gz $mask");
ants-2.1.0/Scripts/antsNeuroimagingBattery-235-
ants-2.1.0/Scripts/antsNeuroimagingBattery:236: system("${ANTSPATH}/ImageMath 3 ${outdir}${dirname}${outname}${outid}md_anatomical.nii.gz TensorMeanDiffusion ${outdir}${dirname}${outname}${outid}dt_anatomical.nii.gz");
ants-2.1.0/Scripts/antsNeuroimagingBattery:237: system("${ANTSPATH}/ImageMath 3 ${outdir}${dirname}${outname}${outid}md_anatomical.nii.gz m ${outdir}${dirname}${outname}${outid}md_anatomical.nii.gz $mask");
ants-2.1.0/Scripts/antsNeuroimagingBattery-238-
ants-2.1.0/Scripts/antsNeuroimagingBattery:239: system("${ANTSPATH}/ImageMath 3 ${outdir}${dirname}${outname}${outid}rd_anatomical.nii.gz TensorRadialDiffusion ${outdir}${dirname}${outname}${outid}dt_anatomical.nii.gz");
ants-2.1.0/Scripts/antsNeuroimagingBattery:240: system("${ANTSPATH}/ImageMath 3 ${outdir}${dirname}${outname}${outid}rd_anatomical.nii.gz m ${outdir}${dirname}${outname}${outid}rd_anatomical.nii.gz $mask");
ants-2.1.0/Scripts/antsNeuroimagingBattery-241-
ants-2.1.0/Scripts/antsNeuroimagingBattery-242- # Remove for space reasons
ants-2.1.0/Scripts/antsNeuroimagingBattery:243: system("rm ${outdir}${dirname}${outname}${outid}dt_anatomical.nii.gz");
ants-2.1.0/Scripts/antsNeuroimagingBattery-244-
ants-2.1.0/Scripts/antsNeuroimagingBattery-245- if ( -s "${outdir}${dirname}${outname}${outid}dt_template.nii.gz") {
ants-2.1.0/Scripts/antsNeuroimagingBattery:246: system("${ANTSPATH}/ImageMath 3 ${outdir}${dirname}${outname}${outid}fa_template.nii.gz TensorFA ${outdir}${dirname}${outname}${outid}dt_template.nii.gz");
ants-2.1.0/Scripts/antsNeuroimagingBattery-247-
ants-2.1.0/Scripts/antsNeuroimagingBattery:248: system("${ANTSPATH}/ImageMath 3 ${outdir}${dirname}${outname}${outid}md_template.nii.gz TensorMeanDiffusion ${outdir}${dirname}${outname}${outid}dt_template.nii.gz");
ants-2.1.0/Scripts/antsNeuroimagingBattery-249-
ants-2.1.0/Scripts/antsNeuroimagingBattery:250: system("${ANTSPATH}/ImageMath 3 ${outdir}${dirname}${outname}${outid}rd_template.nii.gz TensorRadialDiffusion ${outdir}${dirname}${outname}${outid}dt_template.nii.gz");
ants-2.1.0/Scripts/antsNeuroimagingBattery-251-
ants-2.1.0/Scripts/antsNeuroimagingBattery:252: system("rm ${outdir}${dirname}${outname}${outid}dt_template.nii.gz");
ants-2.1.0/Scripts/antsNeuroimagingBattery-253-
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-273- if ( ! -d "${outdir}${dirname}") {
ants-2.1.0/Scripts/antsNeuroimagingBattery:274: `mkdir -p ${outdir}${dirname}`;
ants-2.1.0/Scripts/antsNeuroimagingBattery-275- }
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-284- # Create anatomical reference to align to
ants-2.1.0/Scripts/antsNeuroimagingBattery:285: system("${ANTSPATH}/ImageMath 3 $ref m $anat $mask" );
ants-2.1.0/Scripts/antsNeuroimagingBattery:286: system("${ANTSPATH}/ResampleImageBySpacing 3 $ref $ref 2.0 2.0 2.0");
ants-2.1.0/Scripts/antsNeuroimagingBattery-287-
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-289- my $m0Moco1 = "${ANTSPATH}/antsMotionCorr -d 3 -a $pcaslfile -o $meanpcasl";
ants-2.1.0/Scripts/antsNeuroimagingBattery:290: system($m0Moco1);
ants-2.1.0/Scripts/antsNeuroimagingBattery-291-
ants-2.1.0/Scripts/antsNeuroimagingBattery-292- my $m0Moco2 = "${ANTSPATH}/antsMotionCorr -d 3 -o [ ${outdir}${dirname}${outname}${outid}, $meanpcasl, $meanpcasl ] -u 1 -m mi[ $meanpcasl, $pcaslfile, 1, 32, Regular, 0.1 ] -t Affine[0.2] -i 25 -e 1 -f 1 -s 0 -l 0";
ants-2.1.0/Scripts/antsNeuroimagingBattery:293: system( $m0Moco2 );
ants-2.1.0/Scripts/antsNeuroimagingBattery-294-
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-296- print( "\n\n\n$makecbf\n\n\n");
ants-2.1.0/Scripts/antsNeuroimagingBattery:297: system( $makecbf );
ants-2.1.0/Scripts/antsNeuroimagingBattery-298- }
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-301-
ants-2.1.0/Scripts/antsNeuroimagingBattery:302: system( $alignexe );
ants-2.1.0/Scripts/antsNeuroimagingBattery-303-
ants-2.1.0/Scripts/antsNeuroimagingBattery:304: system("${ANTSPATH}/antsMotionCorrStats -x ${outdir}${dirname}${outname}${outid}brainmask.nii.gz -m ${outdir}${dirname}${outname}${outid}MOCOparams.csv -o ${outdir}${dirname}${outname}${outid}MOCOStatsFramewise.csv -f 1");
ants-2.1.0/Scripts/antsNeuroimagingBattery-305-
ants-2.1.0/Scripts/antsNeuroimagingBattery:306: system("${ANTSPATH}/antsMotionCorrStats -x ${outdir}${dirname}${outname}${outid}brainmask.nii.gz -m ${outdir}${dirname}${outname}${outid}MOCOparams.csv -o ${outdir}${dirname}${outname}${outid}MOCOStatsReference.csv -f 0");
ants-2.1.0/Scripts/antsNeuroimagingBattery-307-
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-330- if ( ! -d "${outdir}${dirname}") {
ants-2.1.0/Scripts/antsNeuroimagingBattery:331: `mkdir -p ${outdir}${dirname}`;
ants-2.1.0/Scripts/antsNeuroimagingBattery-332- }
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-343-
ants-2.1.0/Scripts/antsNeuroimagingBattery:344: system("${ANTSPATH}/ImageMath 3 $ref m $anat $mask" );
ants-2.1.0/Scripts/antsNeuroimagingBattery-345- my $res = "${ANTSPATH}/ResampleImageBySpacing 3 $ref $ref 2.0 2.0 2.0";
ants-2.1.0/Scripts/antsNeuroimagingBattery:346: system($res);
ants-2.1.0/Scripts/antsNeuroimagingBattery-347-
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-349- my $m0Moco1 = "${ANTSPATH}/antsMotionCorr -d 3 -a $m0file -o $meanM0";
ants-2.1.0/Scripts/antsNeuroimagingBattery:350: system($m0Moco1);
ants-2.1.0/Scripts/antsNeuroimagingBattery-351-
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-353- print( "$m0Moco2\n");
ants-2.1.0/Scripts/antsNeuroimagingBattery:354: system( $m0Moco2 );
ants-2.1.0/Scripts/antsNeuroimagingBattery-355-
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-359- #print("$paslMoco\n");
ants-2.1.0/Scripts/antsNeuroimagingBattery:360: #system($paslMoco);
ants-2.1.0/Scripts/antsNeuroimagingBattery-361-
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-363- print( "\n\n\n$makecbf\n\n\n");
ants-2.1.0/Scripts/antsNeuroimagingBattery:364: system( $makecbf );
ants-2.1.0/Scripts/antsNeuroimagingBattery-365- }
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-369-
ants-2.1.0/Scripts/antsNeuroimagingBattery:370: system( $alignexe );
ants-2.1.0/Scripts/antsNeuroimagingBattery-371-
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-389- print( "Create diretory\n");
ants-2.1.0/Scripts/antsNeuroimagingBattery:390: `mkdir -p ${outdir}${dirname}`;
ants-2.1.0/Scripts/antsNeuroimagingBattery-391- }
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-405- my $stc = "${ANTSPATH}/ImageMath 4 $bold SliceTimingCorrection $boldfile 0 bspline";
ants-2.1.0/Scripts/antsNeuroimagingBattery:406: system($stc);
ants-2.1.0/Scripts/antsNeuroimagingBattery-407-
ants-2.1.0/Scripts/antsNeuroimagingBattery-408- # Motion correction
ants-2.1.0/Scripts/antsNeuroimagingBattery:409: system("${ANTSPATH}/antsMotionCorr -d 3 -a $bold -o $meanbold");
ants-2.1.0/Scripts/antsNeuroimagingBattery:410: system("${ANTSPATH}/antsMotionCorr -d 3 -o [ ${obase}, $bold, $meanbold ] -u 1 -m mi[ $meanbold, $bold, 1, 32, Regular, 0.1 ] -t Affine[0.2] -i 25 -e 1 -f 1 -s 0 -l 0 -u 1");
ants-2.1.0/Scripts/antsNeuroimagingBattery-411-
ants-2.1.0/Scripts/antsNeuroimagingBattery-412-
ants-2.1.0/Scripts/antsNeuroimagingBattery:413: system("${ANTSPATH}/ImageMath 3 $ref m $anat $mask" );
ants-2.1.0/Scripts/antsNeuroimagingBattery-414- my $res = "${ANTSPATH}/ResampleImageBySpacing 3 $ref $ref 2.0 2.0 2.0";
ants-2.1.0/Scripts/antsNeuroimagingBattery:415: system($res);
ants-2.1.0/Scripts/antsNeuroimagingBattery-416- }
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-418- my $alignexe = "sh ${ANTSPATH}/antsIntermodalityIntrasubject.sh -d 3 -t 2 -i $meanbold -r $ref -R $anat -x $mask $warpflag -o ${outdir}${dirname}${outname}${outid} -T $template";
ants-2.1.0/Scripts/antsNeuroimagingBattery:419: system( $alignexe );
ants-2.1.0/Scripts/antsNeuroimagingBattery-420-
ants-2.1.0/Scripts/antsNeuroimagingBattery:421: system("${ANTSPATH}/antsMotionCorrStats -x ${outdir}${dirname}${outname}${outid}_brainmask.nii.gz -m ${outdir}${dirname}${outname}${outid}_MOCOparams.csv -0 ${outdir}${dirname}${outname}${outid}_MOCOstats.csv -f 1");
ants-2.1.0/Scripts/antsNeuroimagingBattery-422-
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-435- print( "Create diretory\n");
ants-2.1.0/Scripts/antsNeuroimagingBattery:436: `mkdir -p ${outdir}${dirname}`;
ants-2.1.0/Scripts/antsNeuroimagingBattery-437- }
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-451- # Motion correction
ants-2.1.0/Scripts/antsNeuroimagingBattery:452: system("${ANTSPATH}/antsMotionCorr -d 3 -a $rsboldfile -o $meanbold");
ants-2.1.0/Scripts/antsNeuroimagingBattery-453- print("${ANTSPATH}/antsMotionCorr -d 3 -o [ ${obase}, $bold, $meanbold ] -u 1 -m mi[ $meanbold, $rsboldfile, 1, 32, Regular, 0.1 ] -t Affine[0.2] -i 25 -e 1 -f 1 -s 0 -l 0 -u 1 \n");
ants-2.1.0/Scripts/antsNeuroimagingBattery:454: system("${ANTSPATH}/antsMotionCorr -d 3 -o [ ${obase}, $bold, $meanbold ] -m mi[ $meanbold, $rsboldfile, 1, 32, Regular, 0.1 ] -t Affine[0.2] -i 25 -e 1 -f 1 -s 0 -l 0 -u 1");
ants-2.1.0/Scripts/antsNeuroimagingBattery-455-
ants-2.1.0/Scripts/antsNeuroimagingBattery-456-
ants-2.1.0/Scripts/antsNeuroimagingBattery:457: system("${ANTSPATH}/ImageMath 3 $ref m $anat $mask" );
ants-2.1.0/Scripts/antsNeuroimagingBattery-458- my $res = "${ANTSPATH}/ResampleImageBySpacing 3 $ref $ref 2.0 2.0 2.0";
ants-2.1.0/Scripts/antsNeuroimagingBattery:459: system($res);
ants-2.1.0/Scripts/antsNeuroimagingBattery-460- }
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-462- my $alignexe = "sh ${ANTSPATH}/antsIntermodalityIntrasubject.sh -d 3 -t 2 -i $meanbold -r $ref -R $anat -x $mask $warpflag -o ${outdir}${dirname}${outname}${outid} -T $template";
ants-2.1.0/Scripts/antsNeuroimagingBattery:463: system( $alignexe );
ants-2.1.0/Scripts/antsNeuroimagingBattery-464-
ants-2.1.0/Scripts/antsNeuroimagingBattery:465: system("${ANTSPATH}/antsMotionCorrStats -x ${outdir}${dirname}${outname}${outid}brainmask.nii.gz -m ${outdir}${dirname}${outname}${outid}MOCOparams.csv -o ${outdir}${dirname}${outname}${outid}MOCOStatsFramewise.csv -f 1");
ants-2.1.0/Scripts/antsNeuroimagingBattery-466-
ants-2.1.0/Scripts/antsNeuroimagingBattery:467: system("${ANTSPATH}/antsMotionCorrStats -x ${outdir}${dirname}${outname}${outid}brainmask.nii.gz -m ${outdir}${dirname}${outname}${outid}MOCOparams.csv -o ${outdir}${dirname}${outname}${outid}MOCOStatsReference.csv -f 0");
ants-2.1.0/Scripts/antsNeuroimagingBattery-468- }
##############################################
ants-2.1.0/Scripts/antsRegistrationSyN.sh-21-
ants-2.1.0/Scripts/antsRegistrationSyN.sh:22:Alternatively, edit this script ( `basename $0` ) to set up this parameter correctly.
ants-2.1.0/Scripts/antsRegistrationSyN.sh-23-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyN.sh-49-
ants-2.1.0/Scripts/antsRegistrationSyN.sh:50:`basename $0` -d ImageDimension -f FixedImage -m MovingImage -o OutputPrefix
ants-2.1.0/Scripts/antsRegistrationSyN.sh-51-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyN.sh-91-
ants-2.1.0/Scripts/antsRegistrationSyN.sh:92:`basename $0` -d 3 -f fixedImage.nii.gz -m movingImage.nii.gz -o output
ants-2.1.0/Scripts/antsRegistrationSyN.sh-93-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyN.sh-111-
ants-2.1.0/Scripts/antsRegistrationSyN.sh:112:`basename $0` -d ImageDimension -f FixedImage -m MovingImage -o OutputPrefix
ants-2.1.0/Scripts/antsRegistrationSyN.sh-113-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyN.sh-115-
ants-2.1.0/Scripts/antsRegistrationSyN.sh:116:`basename $0` -d 3 -f fixedImage.nii.gz -m movingImage.nii.gz -o output
ants-2.1.0/Scripts/antsRegistrationSyN.sh-117-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyN.sh-215-# put all related processes in array
ants-2.1.0/Scripts/antsRegistrationSyN.sh:216:runningANTSpids=( `ps -C antsRegistration | awk '{ printf "%s\n", $1 ; }'` )
ants-2.1.0/Scripts/antsRegistrationSyN.sh-217-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyN.sh-362-SIZESTRING="${SIZESTRING%\\n}"
ants-2.1.0/Scripts/antsRegistrationSyN.sh:363:SIZE=( `echo $SIZESTRING | tr 'x' ' '` )
ants-2.1.0/Scripts/antsRegistrationSyN.sh-364-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-21-
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh:22:Alternatively, edit this script ( `basename $0` ) to set up this parameter correctly.
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-23-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-49-
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh:50:`basename $0` -d ImageDimension -f FixedImage -m MovingImage -o OutputPrefix
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-51-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-90-
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh:91:`basename $0` -d 3 -f fixedImage.nii.gz -m movingImage.nii.gz -o output
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-92-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-110-
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh:111:`basename $0` -d ImageDimension -f FixedImage -m MovingImage -o OutputPrefix
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-112-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-114-
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh:115:`basename $0` -d 3 -f fixedImage.nii.gz -m movingImage.nii.gz -o output
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-116-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-214-# put all related processes in array
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh:215:runningANTSpids=( `ps -C antsRegistration | awk '{ printf "%s\n", $1 ; }'` )
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-216-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-361-SIZESTRING="${SIZESTRING%\\n}"
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh:362:SIZE=( `echo $SIZESTRING | tr 'x' ' '` )
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-363-
##############################################
ants-2.1.0/Scripts/antsaffine.sh-59-
ants-2.1.0/Scripts/antsaffine.sh:60:OUTPUTNAME=` echo $MOVING | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsaffine.sh-61-
##############################################
ants-2.1.0/Scripts/antsbashstats.sh-93-stat_median() {
ants-2.1.0/Scripts/antsbashstats.sh:94: NUMS=(`sort -n $1`)
ants-2.1.0/Scripts/antsbashstats.sh-95- TOTALNUMS=${#NUMS[*]}
##############################################
ants-2.1.0/Scripts/antsdeformationmag.sh-16-ANTSPATH=$4
ants-2.1.0/Scripts/antsdeformationmag.sh:17:dimarr=(`${ANTSPATH}/PrintHeader ${inwarp}xvec.nii.gz | grep Spacing | grep , | wc `)
ants-2.1.0/Scripts/antsdeformationmag.sh-18-DIM=${dimarr[0]}
##############################################
ants-2.1.0/Scripts/antswithdt.sh-100- TRANSFORMATION=SyN[0.25]
ants-2.1.0/Scripts/antswithdt.sh:101: ITERATLEVEL=(`echo $MAXITERATIONS | tr 'x' ' '`)
ants-2.1.0/Scripts/antswithdt.sh-102- NUMLEVELS=${#ITERATLEVEL[@]}
##############################################
ants-2.1.0/Scripts/basic_ants_example.sh-134-TEM=${OUTPUTNAME}BTPtemplate.nii.gz
ants-2.1.0/Scripts/basic_ants_example.sh:135:NM1=` echo $JJ | cut -d '.' -f 1 `
ants-2.1.0/Scripts/basic_ants_example.sh-136-INVW=" -i ${OUTPUTNAME}BTP${NM1}Affine.txt ${OUTPUTNAME}BTP${NM1}InverseWarp.nii.gz "
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-21-
ants-2.1.0/Scripts/buildtemplateparallel.sh:22:Alternatively, edit this script ( `basename $0` ) to set up this parameter correctly.
ants-2.1.0/Scripts/buildtemplateparallel.sh-23-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-74-
ants-2.1.0/Scripts/buildtemplateparallel.sh:75:`basename $0` -d ImageDimension -o OUTPREFIX <other options> <images>
ants-2.1.0/Scripts/buildtemplateparallel.sh-76-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-126-
ants-2.1.0/Scripts/buildtemplateparallel.sh:127:`basename $0` -d 3 -m 30x50x20 -t GR -s CC -c 1 -o MY -z InitialTemplate.nii.gz *RF*T1x.nii.gz
ants-2.1.0/Scripts/buildtemplateparallel.sh-128-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-164-
ants-2.1.0/Scripts/buildtemplateparallel.sh:165:`basename $0` will make a template out of the input files using an elastic
ants-2.1.0/Scripts/buildtemplateparallel.sh-166-or diffeomorphic transformation. This script builds a template iteratively from the input
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-171-
ants-2.1.0/Scripts/buildtemplateparallel.sh:172:`basename $0` -d ImageDimension -o OUTPREFIX <other options> <images>
ants-2.1.0/Scripts/buildtemplateparallel.sh-173-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-175-
ants-2.1.0/Scripts/buildtemplateparallel.sh:176: bash `basename $0` -d 3 -m 30x50x20 -t GR -s CC -c 1 -o MY -z InitialTemplate.nii.gz *RF*T1x.nii.gz
ants-2.1.0/Scripts/buildtemplateparallel.sh-177-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-377-
ants-2.1.0/Scripts/buildtemplateparallel.sh:378: ${ANTSPATH}/AverageImages $dim ${templatename}warp.nii.gz 0 `ls ${outputname}*Warp.nii.gz | grep -v "InverseWarp"`
ants-2.1.0/Scripts/buildtemplateparallel.sh-379-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-433- PARAM8=0
ants-2.1.0/Scripts/buildtemplateparallel.sh:434: LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 2 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:435: for x in $LL ; do PARAM1=` awk -v a=$PARAM1 -v b=$x 'BEGIN{print (a + b)}' ` ; let NFILES=$NFILES+1 ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:436: PARAM1=` awk -v a=$PARAM1 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-437-
ants-2.1.0/Scripts/buildtemplateparallel.sh:438: LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 3 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:439: for x in $LL ; do PARAM2=` awk -v a=$PARAM2 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:440: PARAM2=` awk -v a=$PARAM2 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-441-
ants-2.1.0/Scripts/buildtemplateparallel.sh:442: LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 4 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:443: for x in $LL ; do PARAM3=` awk -v a=$PARAM3 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:444: PARAM3=` awk -v a=$PARAM3 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-445-
ants-2.1.0/Scripts/buildtemplateparallel.sh:446: LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 5 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:447: for x in $LL ; do PARAM4=` awk -v a=$PARAM4 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:448: PARAM4=` awk -v a=$PARAM4 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-449-
ants-2.1.0/Scripts/buildtemplateparallel.sh:450: LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 6 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:451: for x in $LL ; do PARAM5=` awk -v a=$PARAM5 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:452: PARAM5=0 # ` awk -v a=$PARAM5 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-453-
ants-2.1.0/Scripts/buildtemplateparallel.sh:454: LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 7 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:455: for x in $LL ; do PARAM6=` awk -v a=$PARAM6 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:456: PARAM6=0 # ` awk -v a=$PARAM6 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-457-
ants-2.1.0/Scripts/buildtemplateparallel.sh:458: LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 2 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:459: for x in $LL ; do PARAM7=` awk -v a=$PARAM7 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:460: PARAM7=` awk -v a=$PARAM7 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-461-
ants-2.1.0/Scripts/buildtemplateparallel.sh:462: LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 3 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:463: for x in $LL ; do PARAM8=` awk -v a=$PARAM8 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:464: PARAM8=` awk -v a=$PARAM8 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-465-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-492- PARAM15=0
ants-2.1.0/Scripts/buildtemplateparallel.sh:493: LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 2 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:494: for x in $LL ; do PARAM1=` awk -v a=$PARAM1 -v b=$x 'BEGIN{print (a + b)}' ` ; let NFILES=$NFILES+1 ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:495: PARAM1=` awk -v a=$PARAM1 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-496-
ants-2.1.0/Scripts/buildtemplateparallel.sh:497: LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 3 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:498: for x in $LL ; do PARAM2=` awk -v a=$PARAM2 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:499: PARAM2=` awk -v a=$PARAM2 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-500-
ants-2.1.0/Scripts/buildtemplateparallel.sh:501: LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 4 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:502: for x in $LL ; do PARAM3=` awk -v a=$PARAM3 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:503: PARAM3=` awk -v a=$PARAM3 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-504-
ants-2.1.0/Scripts/buildtemplateparallel.sh:505: LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 5 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:506: for x in $LL ; do PARAM4=` awk -v a=$PARAM4 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:507: PARAM4=` awk -v a=$PARAM4 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-508-
ants-2.1.0/Scripts/buildtemplateparallel.sh:509: LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 6 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:510: for x in $LL ; do PARAM5=` awk -v a=$PARAM5 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:511: PARAM5=` awk -v a=$PARAM5 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-512-
ants-2.1.0/Scripts/buildtemplateparallel.sh:513: LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 7 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:514: for x in $LL ; do PARAM6=` awk -v a=$PARAM6 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:515: PARAM6=` awk -v a=$PARAM6 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-516-
ants-2.1.0/Scripts/buildtemplateparallel.sh:517: LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 8 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:518: for x in $LL ; do PARAM7=` awk -v a=$PARAM7 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:519: PARAM7=` awk -v a=$PARAM7 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-520-
ants-2.1.0/Scripts/buildtemplateparallel.sh:521: LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 9 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:522: for x in $LL ; do PARAM8=` awk -v a=$PARAM8 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:523: PARAM8=` awk -v a=$PARAM8 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-524-
ants-2.1.0/Scripts/buildtemplateparallel.sh:525: LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 10 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:526: for x in $LL ; do PARAM9=` awk -v a=$PARAM9 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:527: PARAM9=` awk -v a=$PARAM9 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-528-
ants-2.1.0/Scripts/buildtemplateparallel.sh:529: LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 11 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:530: for x in $LL ; do PARAM10=` awk -v a=$PARAM10 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:531: PARAM10=0 # ` awk -v a=$PARAM10 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-532-
ants-2.1.0/Scripts/buildtemplateparallel.sh:533: LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 12 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:534: for x in $LL ; do PARAM11=` awk -v a=$PARAM11 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:535: PARAM11=0 # ` awk -v a=$PARAM11 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-536-
ants-2.1.0/Scripts/buildtemplateparallel.sh:537: LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 13 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:538: for x in $LL ; do PARAM12=` awk -v a=$PARAM12 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:539: PARAM12=0 # ` awk -v a=$PARAM12 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-540-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-542-
ants-2.1.0/Scripts/buildtemplateparallel.sh:543: LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 2 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:544: for x in $LL ; do PARAM13=` awk -v a=$PARAM13 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:545: PARAM13=` awk -v a=$PARAM13 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-546-
ants-2.1.0/Scripts/buildtemplateparallel.sh:547: LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 3 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:548: for x in $LL ; do PARAM14=` awk -v a=$PARAM14 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:549: PARAM14=` awk -v a=$PARAM14 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-550-
ants-2.1.0/Scripts/buildtemplateparallel.sh:551: LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 4 `
ants-2.1.0/Scripts/buildtemplateparallel.sh:552: for x in $LL ; do PARAM15=` awk -v a=$PARAM15 -v b=$x 'BEGIN{print (a + b)}' ` ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:553: PARAM15=` awk -v a=$PARAM15 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-554-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-565- files=`ls job*.sh`
ants-2.1.0/Scripts/buildtemplateparallel.sh:566: BASENAME1=`echo $files[1] | cut -d 'b' -f 1`
ants-2.1.0/Scripts/buildtemplateparallel.sh-567-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-572- then
ants-2.1.0/Scripts/buildtemplateparallel.sh:573: BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/buildtemplateparallel.sh-574- mv "$file" "${BASENAME1}b_000${BASENAME2}"
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-577- then
ants-2.1.0/Scripts/buildtemplateparallel.sh:578: BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/buildtemplateparallel.sh-579- mv "$file" "${BASENAME1}b_00${BASENAME2}"
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-582- then
ants-2.1.0/Scripts/buildtemplateparallel.sh:583: BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/buildtemplateparallel.sh-584- mv "$file" "${BASENAME1}b_0${BASENAME2}"
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-599-# put all related processes in array
ants-2.1.0/Scripts/buildtemplateparallel.sh:600: runningANTSpids=( `ps -C ANTS -C N4BiasFieldCorrection -C ImageMath| awk '{ printf "%s\n", $1 ; }'` )
ants-2.1.0/Scripts/buildtemplateparallel.sh-601-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-659-##Getting system info from linux can be done with these variables.
ants-2.1.0/Scripts/buildtemplateparallel.sh:660:# RAM=`cat /proc/meminfo | sed -n -e '/MemTotal/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
ants-2.1.0/Scripts/buildtemplateparallel.sh:661:# RAMfree=`cat /proc/meminfo | sed -n -e '/MemFree/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
ants-2.1.0/Scripts/buildtemplateparallel.sh-662-# cpu_free_ram=$((${RAMfree}/${cpu_count}))
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-785- echo "Please provide at least 2 filenames for the template."
ants-2.1.0/Scripts/buildtemplateparallel.sh:786: echo "Use `basename $0` -h for help"
ants-2.1.0/Scripts/buildtemplateparallel.sh-787- exit 1
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-790-
ants-2.1.0/Scripts/buildtemplateparallel.sh:791: range=`${ANTSPATH}/ImageMath $TDIM abs nvols ${IMAGESETVARIABLE} | tail -1 | cut -d "," -f 4 | cut -d " " -f 2 | cut -d "]" -f 1 `
ants-2.1.0/Scripts/buildtemplateparallel.sh-792-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-795- echo "Please provide at least 2 filenames for the template."
ants-2.1.0/Scripts/buildtemplateparallel.sh:796: echo "Use `basename $0` -h for help"
ants-2.1.0/Scripts/buildtemplateparallel.sh-797- exit 1
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-800- echo "This is a multivolume file. Use -d 4"
ants-2.1.0/Scripts/buildtemplateparallel.sh:801: echo "Use `basename $0` -h for help"
ants-2.1.0/Scripts/buildtemplateparallel.sh-802- exit 1
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-949-
ants-2.1.0/Scripts/buildtemplateparallel.sh:950: BASENAME=` echo ${IMG} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/buildtemplateparallel.sh-951-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-964- if [ $DOQSUB -eq 1 ] ; then
ants-2.1.0/Scripts/buildtemplateparallel.sh:965: id=`qsub -cwd -S /bin/bash -N antsBuildTemplate_rigid -v ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1,LD_LIBRARY_PATH=$LD_LIBRARY_PATH,ANTSPATH=$ANTSPATH $QSUBOPTS $qscript | awk '{print $3}'`
ants-2.1.0/Scripts/buildtemplateparallel.sh-966- jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-969- echo "cp -R /jobtmp/pbstmp.\$PBS_JOBID/* ${currentdir}" >> $qscript;
ants-2.1.0/Scripts/buildtemplateparallel.sh:970: id=`qsub -N antsrigid -v ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1,LD_LIBRARY_PATH=$LD_LIBRARY_PATH,ANTSPATH=$ANTSPATH $QSUBOPTS -q nopreempt -l nodes=1:ppn=1 -l walltime=4:00:00 $qscript | awk '{print $1}'`
ants-2.1.0/Scripts/buildtemplateparallel.sh-971- jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-977- elif [ $DOQSUB -eq 3 ] ; then
ants-2.1.0/Scripts/buildtemplateparallel.sh:978: id=`xgrid $XGRIDOPTS -job submit /bin/bash $qscript | awk '{sub(/;/,"");print $3}' | tr '\n' ' ' | sed 's: *: :g'`
ants-2.1.0/Scripts/buildtemplateparallel.sh-979- #echo "xgrid $XGRIDOPTS -job submit /bin/bash $qscript"
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-1090-# Begin Main Loop
ants-2.1.0/Scripts/buildtemplateparallel.sh:1091:ITERATLEVEL=(` echo $MAXITERATIONS | tr 'x' ' ' `)
ants-2.1.0/Scripts/buildtemplateparallel.sh-1092-NUMLEVELS=${#ITERATLEVEL[@]}
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-1164- if [ $DOQSUB -eq 1 ]; then
ants-2.1.0/Scripts/buildtemplateparallel.sh:1165: id=`qsub -cwd -N antsBuildTemplate_deformable_${i} -S /bin/bash -v ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1,LD_LIBRARY_PATH=$LD_LIBRARY_PATH,ANTSPATH=$ANTSPATH $QSUBOPTS $exe | awk '{print $3}'`
ants-2.1.0/Scripts/buildtemplateparallel.sh-1166- jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-1172- echo "cp -R /jobtmp/pbstmp.\$PBS_JOBID/* ${currentdir}" >> $qscript;
ants-2.1.0/Scripts/buildtemplateparallel.sh:1173: id=`qsub -N antsdef${i} -v ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1,LD_LIBRARY_PATH=$LD_LIBRARY_PATH,ANTSPATH=$ANTSPATH -q nopreempt -l nodes=1:ppn=1 -l walltime=4:00:00 $QSUBOPTS $qscript | awk '{print $1}'`
ants-2.1.0/Scripts/buildtemplateparallel.sh-1174- jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-1183- echo "$exe" >> $qscript
ants-2.1.0/Scripts/buildtemplateparallel.sh:1184: id=`xgrid $XGRIDOPTS -job submit /bin/bash $qscript | awk '{sub(/;/,"");print $3}' | tr '\n' ' ' | sed 's: *: :g'`
ants-2.1.0/Scripts/buildtemplateparallel.sh-1185- jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-1190- # counter updated, but not directly used in this loop
ants-2.1.0/Scripts/buildtemplateparallel.sh:1191: count=`expr $count + 1`;
ants-2.1.0/Scripts/buildtemplateparallel.sh-1192-
##############################################
ants-2.1.0/Scripts/directlabels.sh-25-
ants-2.1.0/Scripts/directlabels.sh:26:`basename $0` -d ImageDimension -s InputSegmentationImage -l CorticalLabelImage <OPTARGS> -o OutputImage
ants-2.1.0/Scripts/directlabels.sh-27-
##############################################
ants-2.1.0/Scripts/directlabels.sh-84-
ants-2.1.0/Scripts/directlabels.sh:85: OUTPUT=(`${ANTSPATH}/LabelGeometryMeasures $DIMENSION $LABEL_IMAGE`);
ants-2.1.0/Scripts/directlabels.sh-86-
##############################################
ants-2.1.0/Scripts/directlabels.sh-89- begin=10
ants-2.1.0/Scripts/directlabels.sh:90: increment=`expr 5 + $DIMENSION + $DIMENSION + $DIMENSION + $DIMENSION`
ants-2.1.0/Scripts/directlabels.sh-91-
##############################################
ants-2.1.0/Scripts/directlabels.sh-94- LABELS[$count]=${OUTPUT[$i]}
ants-2.1.0/Scripts/directlabels.sh:95: count=`expr $count + 1`
ants-2.1.0/Scripts/directlabels.sh-96- done
##############################################
ants-2.1.0/Scripts/directlabels.sh-98- ## Get bounding boxes
ants-2.1.0/Scripts/directlabels.sh:99: begin=`expr 15 + $DIMENSION + $DIMENSION`
ants-2.1.0/Scripts/directlabels.sh:100: increment=`expr 5 + $DIMENSION + $DIMENSION + $DIMENSION + $DIMENSION`
ants-2.1.0/Scripts/directlabels.sh-101-
##############################################
ants-2.1.0/Scripts/directlabels.sh-103- for (( i=begin; i<=${#OUTPUT[@]}; i+=$increment )); do
ants-2.1.0/Scripts/directlabels.sh:104: for (( j=0; j<`expr $DIMENSION + $DIMENSION`; j++ )); do
ants-2.1.0/Scripts/directlabels.sh:105: BOUNDING_BOXES[$count]=${BOUNDING_BOXES[$count]}${OUTPUT[`expr $i+$j`]}
ants-2.1.0/Scripts/directlabels.sh-106- done
ants-2.1.0/Scripts/directlabels.sh:107: count=`expr $count + 1`;
ants-2.1.0/Scripts/directlabels.sh-108- done
##############################################
ants-2.1.0/Scripts/directlabels.sh-110- ## read thickness .csv file if it exists
ants-2.1.0/Scripts/directlabels.sh:111: extension=`echo ${THICKNESS_PRIOR_ESTIMATE#*.}`
ants-2.1.0/Scripts/directlabels.sh-112-
##############################################
ants-2.1.0/Scripts/directlabels.sh-117- do
ants-2.1.0/Scripts/directlabels.sh:118: bar=(`echo $line | tr ',' ' '`)
ants-2.1.0/Scripts/directlabels.sh-119-
##############################################
ants-2.1.0/Scripts/directlabels.sh-158-
ants-2.1.0/Scripts/directlabels.sh:159: jp1=`expr $j + 1`
ants-2.1.0/Scripts/directlabels.sh-160- maxValue=${elements[$jp1]}
##############################################
ants-2.1.0/Scripts/directlabels.sh-164-
ants-2.1.0/Scripts/directlabels.sh:165: count=`expr $count + 1`
ants-2.1.0/Scripts/directlabels.sh-166- done
##############################################
ants-2.1.0/Scripts/directlabels.sh-180- #
ants-2.1.0/Scripts/directlabels.sh:181: OUTPUT=(`${ANTSPATH}/ThresholdImage $DIMENSION $LABEL_IMAGE $grayMatterMask ${LABELS[$i]} ${LABELS[$i]} 1 0`)
ants-2.1.0/Scripts/directlabels.sh:182: OUTPUT=(`${ANTSPATH}/ThresholdImage $DIMENSION $SEG_IMAGE $whiteMatterMask 3 3 3 0`)
ants-2.1.0/Scripts/directlabels.sh:183: OUTPUT=(`${ANTSPATH}/ImageMath $DIMENSION $grayMatterMask m $grayMatterMask $SEG_IMAGE`)
ants-2.1.0/Scripts/directlabels.sh:184: OUTPUT=(`${ANTSPATH}/ImageMath $DIMENSION $gmWmMask + $grayMatterMask $whiteMatterMask`)
ants-2.1.0/Scripts/directlabels.sh:185: OUTPUT=(`${ANTSPATH}/ExtractRegionFromImage $DIMENSION $gmWmMask ${TMPDIR}seg_${LABELS[$i]}.nii.gz $minIndex $maxIndex`)
ants-2.1.0/Scripts/directlabels.sh:186: OUTPUT=(`${ANTSPATH}/ImageMath $DIMENSION ${TMPDIR}seg_${LABELS[$i]}.nii.gz PadImage ${TMPDIR}seg_${LABELS[$i]}.nii.gz $PADDING`)
ants-2.1.0/Scripts/directlabels.sh-187- if [ -f $WMPROB_IMAGE ]; then
ants-2.1.0/Scripts/directlabels.sh:188: OUTPUT=(`${ANTSPATH}/ImageMath $DIMENSION $whiteMatterMask m $whiteMatterMask $WMPROB_IMAGE`)
ants-2.1.0/Scripts/directlabels.sh:189: OUTPUT=(`${ANTSPATH}/ExtractRegionFromImage $DIMENSION $whiteMatterMask ${TMPDIR}wm_${LABELS[$i]}.nii.gz $minIndex $maxIndex`);
ants-2.1.0/Scripts/directlabels.sh:190: OUTPUT=(`${ANTSPATH}/ImageMath $DIMENSION ${TMPDIR}wm_${LABELS[$i]}.nii.gz PadImage ${TMPDIR}wm_${LABELS[$i]}.nii.gz $PADDING`);
ants-2.1.0/Scripts/directlabels.sh-191- fi
ants-2.1.0/Scripts/directlabels.sh-192- if [ -f $GMPROB_IMAGE ]; then
ants-2.1.0/Scripts/directlabels.sh:193: OUTPUT=(`${ANTSPATH}/ImageMath $DIMENSION $grayMatterMask m $grayMatterMask $GMPROB_IMAGE`)
ants-2.1.0/Scripts/directlabels.sh:194: OUTPUT=(`${ANTSPATH}/ExtractRegionFromImage $DIMENSION $grayMatterMask ${TMPDIR}gm_${LABELS[$i]}.nii.gz $minIndex $maxIndex`);
ants-2.1.0/Scripts/directlabels.sh:195: OUTPUT=(`${ANTSPATH}/ImageMath $DIMENSION ${TMPDIR}gm_${LABELS[$i]}.nii.gz PadImage ${TMPDIR}gm_${LABELS[$i]}.nii.gz $PADDING`);
ants-2.1.0/Scripts/directlabels.sh-196- fi
##############################################
ants-2.1.0/Scripts/directlabels.sh-206-
ants-2.1.0/Scripts/directlabels.sh:207: files=`ls ${TMPDIR}job*.sh`
ants-2.1.0/Scripts/directlabels.sh:208: BASENAME1=`echo $files[1] | cut -d 'b' -f 1`
ants-2.1.0/Scripts/directlabels.sh-209-
##############################################
ants-2.1.0/Scripts/directlabels.sh-214- then
ants-2.1.0/Scripts/directlabels.sh:215: BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/directlabels.sh-216- mv "$file" "${BASENAME1}b_000${BASENAME2}"
##############################################
ants-2.1.0/Scripts/directlabels.sh-219- then
ants-2.1.0/Scripts/directlabels.sh:220: BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/directlabels.sh-221- mv "$file" "${BASENAME1}b_00${BASENAME2}"
##############################################
ants-2.1.0/Scripts/directlabels.sh-224- then
ants-2.1.0/Scripts/directlabels.sh:225: BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/directlabels.sh-226- mv "$file" "${BASENAME1}b_0${BASENAME2}"
##############################################
ants-2.1.0/Scripts/directlabels.sh-232-
ants-2.1.0/Scripts/directlabels.sh:233: output=( `${ANTSPATH}/CreateImage $DIMENSION $SEG_IMAGE $OUTPUT_IMAGE 0` );
ants-2.1.0/Scripts/directlabels.sh-234-
##############################################
ants-2.1.0/Scripts/directlabels.sh-246- minValue=${elements[$j]}
ants-2.1.0/Scripts/directlabels.sh:247: minValue=`expr $minValue - $PADDING`;
ants-2.1.0/Scripts/directlabels.sh-248-
##############################################
ants-2.1.0/Scripts/directlabels.sh-250-
ants-2.1.0/Scripts/directlabels.sh:251: count=`expr $count + 1`
ants-2.1.0/Scripts/directlabels.sh-252- done
##############################################
ants-2.1.0/Scripts/directlabels.sh-255-
ants-2.1.0/Scripts/directlabels.sh:256: output=(`${ANTSPATH}/PasteImageIntoImage $DIMENSION $OUTPUT_IMAGE $TMPDIR/direct_${LABELS[$i]}.nii.gz $OUTPUT_IMAGE $minIndex 0 2 -1`);
ants-2.1.0/Scripts/directlabels.sh-257- done
##############################################
ants-2.1.0/Scripts/directlabels.sh-409- if [ $DOQSUB -eq 1 ]; then
ants-2.1.0/Scripts/directlabels.sh:410: id=`qsub -cwd -N DiReCT_${LABEL} -S /bin/bash -v ANTSPATH=$ANTSPATH $QSUBOPTS $exe | awk '{print $3}'`
ants-2.1.0/Scripts/directlabels.sh-411- jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/directlabels.sh-417- echo " Performing DiReCT for label ${LABEL}."
ants-2.1.0/Scripts/directlabels.sh:418: output=(`$exe`)
ants-2.1.0/Scripts/directlabels.sh-419- fi
##############################################
ants-2.1.0/Scripts/directlabels.sh-436- fi
ants-2.1.0/Scripts/directlabels.sh:437: count=`expr $count + 1`
ants-2.1.0/Scripts/directlabels.sh-438-done
##############################################
ants-2.1.0/Scripts/lohmann.sh-42-
ants-2.1.0/Scripts/lohmann.sh:43:OUTPUTNAME=` echo $FIXED | cut -d '.' -f 1 `
ants-2.1.0/Scripts/lohmann.sh-44-
##############################################
ants-2.1.0/Scripts/newAntsExample.sh-16-fi
ants-2.1.0/Scripts/newAntsExample.sh:17:nm1=` basename $f | cut -d '.' -f 1 `
ants-2.1.0/Scripts/newAntsExample.sh:18:nm2=` basename $m | cut -d '.' -f 1 `
ants-2.1.0/Scripts/newAntsExample.sh-19-reg=${AP}antsRegistration # path to antsRegistration
##############################################
ants-2.1.0/Scripts/phantomstudy.sh-8-do
ants-2.1.0/Scripts/phantomstudy.sh:9: count=`expr $count + 1` # Increment the counter
ants-2.1.0/Scripts/phantomstudy.sh-10- echo " count is $count and file is $x "
##############################################
ants-2.1.0/Scripts/phantomstudy.sh-24-do
ants-2.1.0/Scripts/phantomstudy.sh:25: count=`expr $count + 1` # Increment the counter
ants-2.1.0/Scripts/phantomstudy.sh-26- echo " count is $count and file is $x "
##############################################
ants-2.1.0/Scripts/registerimages.pl-47- system $waitcmd;
ants-2.1.0/Scripts/registerimages.pl:48: $output = `$waitcmd`;
ants-2.1.0/Scripts/registerimages.pl-49-
##############################################
ants-2.1.0/Scripts/sccan_tests-21-params=" -e 0 -n 2 -i 20 -r 0 -p 0 " # most common parameters
ants-2.1.0/Scripts/sccan_tests:22:t1=`${PATHTOSCCAN}/sccan --scca two-view[ ${PATHTODATA}myview1.csv , ${PATHTODATA}myview_mismatch.csv , na , na , 0.5 , 0.5 ] -o ${OUT}.nii.gz $params `
ants-2.1.0/Scripts/sccan_tests-23-test1=$?
ants-2.1.0/Scripts/sccan_tests:24:t2=`${PATHTOSCCAN}/sccan --svd sparse[ ${PATHTODATA}myview3.csv , na , -0.15 ] -o ${OUT}.nii.gz -n 15 -i 500 `
ants-2.1.0/Scripts/sccan_tests-25-# ${PATHTOSCCAN}/sccan --svd sparse[ ${PATHTODATA}myview3.csv , na , -0.15 ] -o ${OUT}.nii.gz -n 15 -i 500
##############################################
ants-2.1.0/Scripts/sccan_tests-27-paramsb=" -e 0 -n 2 -i 50 -r 0 -p 0 --partial-scca-option PQminusR " # most common parameters
ants-2.1.0/Scripts/sccan_tests:28:t3=`${PATHTOSCCAN}/sccan --scca partial[ ${PATHTODATA}myview2.csv , ${PATHTODATA}myview3.csv , ${PATHTODATA}myview4.csv , na , na , na , -0.4 , -0.9 , 1] -o ${OUT}.nii.gz $paramsb `
ants-2.1.0/Scripts/sccan_tests-29-test3=$?
ants-2.1.0/Scripts/sccan_tests:30:t4=`${PATHTOSCCAN}/sccan --svd sparse[ ${PATHTODATA}myview1.csv , na , 0.5 ] -o ${OUT}.nii.gz `
ants-2.1.0/Scripts/sccan_tests-31-# ${PATHTOSCCAN}/sccan --sparse-svd [ ${PATHTODATA}myview1.csv , na , -1] -o ${OUT}.nii.gz -n 25 -i 1000
##############################################
ants-2.1.0/Scripts/sccan_tests-33-test4=$?
ants-2.1.0/Scripts/sccan_tests:34:t5a=`${PATHTOSCCAN}/sccan --scca partial[ ${PATHTODATA}myview2.csv , ${PATHTODATA}myview3.csv , ${PATHTODATA}myview4.csv , na , na , na , -0.05 , 0.1 , 1] -o ${OUT}.nii.gz $paramsb`
ants-2.1.0/Scripts/sccan_tests:35:t5b=`${PATHTOSCCAN}/sccan --scca partial[ ${PATHTODATA}myview2.csv , ${PATHTODATA}myview3.csv , ${PATHTODATA}myview4.csv , na , na , na , -0.05 , 0.1 , 1] -o ${OUT}.nii.gz $paramsb`
ants-2.1.0/Scripts/sccan_tests-36-echo $t5a > tempa.txt
##############################################
ants-2.1.0/Scripts/sccan_tests-43-rm tempa.txt tempb.txt
ants-2.1.0/Scripts/sccan_tests:44:t5a=`${PATHTOSCCAN}/sccan --scca partial[ ${PATHTODATA}myview2.csv , ${PATHTODATA}myview3.csv , ${PATHTODATA}myview4.csv , na , na , na , 0.05 , 0.1 , 1] -o ${OUT}.nii.gz $paramsb`
ants-2.1.0/Scripts/sccan_tests:45:t5b=`${PATHTOSCCAN}/sccan --scca partial[ ${PATHTODATA}myview2.csv , ${PATHTODATA}myview3.csv , ${PATHTODATA}myview4.csv , na , na , na , -0.05 , 0.1 , 1] -o ${OUT}.nii.gz $paramsb`
ants-2.1.0/Scripts/sccan_tests-46-echo $t5a > tempa.txt
##############################################
ants-2.1.0/Scripts/shapeupdatetotemplate.sh-19-
ants-2.1.0/Scripts/shapeupdatetotemplate.sh:20:Alternatively, edit this script ( `basename $0` ) to set up this parameter correctly.
ants-2.1.0/Scripts/shapeupdatetotemplate.sh-21-
##############################################
ants-2.1.0/Scripts/shapeupdatetotemplate.sh-172- echo "--------------------------------------------------------------------------------------"
ants-2.1.0/Scripts/shapeupdatetotemplate.sh:173: imagelist=(`ls ${outputname}template${whichtemplate}*WarpedToTemplate.nii.gz`)
ants-2.1.0/Scripts/shapeupdatetotemplate.sh-174- if [[ ${#imagelist[@]} -eq 0 ]] ; then
##############################################
ants-2.1.0/Scripts/shapeupdatetotemplate.sh-180-
ants-2.1.0/Scripts/shapeupdatetotemplate.sh:181: WARPLIST=( `ls ${outputname}*[0-9]Warp.nii.gz 2> /dev/null` )
ants-2.1.0/Scripts/shapeupdatetotemplate.sh-182- NWARPS=${#WARPLIST[*]}
##############################################
ants-2.1.0/Scripts/shapeupdatetotemplate.sh-193- echo " shapeupdatetotemplate---voxel-wise averaging of the inverse warp fields (from subject to template)"
ants-2.1.0/Scripts/shapeupdatetotemplate.sh:194: echo " ${ANTSPATH}/AverageImages $dim ${templatename}${whichtemplate}warp.nii.gz 0 `ls ${outputname}*Warp.nii.gz | grep -v "InverseWarp"`"
ants-2.1.0/Scripts/shapeupdatetotemplate.sh-195- date
ants-2.1.0/Scripts/shapeupdatetotemplate.sh-196- echo "--------------------------------------------------------------------------------------"
ants-2.1.0/Scripts/shapeupdatetotemplate.sh:197: ${ANTSPATH}/AverageImages $dim ${templatename}${whichtemplate}warp.nii.gz 0 `ls ${outputname}*Warp.nii.gz | grep -v "InverseWarp"`
ants-2.1.0/Scripts/shapeupdatetotemplate.sh-198-
##############################################
ants-2.1.0/Scripts/thickstudy.sh-5-do
ants-2.1.0/Scripts/thickstudy.sh:6: count=`expr $count + 1` # Increment the counter
ants-2.1.0/Scripts/thickstudy.sh-7- echo " $x "
##############################################
ants-2.1.0/Scripts/waitForPBSQJobs.pl-37-
ants-2.1.0/Scripts/waitForPBSQJobs.pl:38:my $qstatOutput = `qstat -u $user`;
ants-2.1.0/Scripts/waitForPBSQJobs.pl-39-
##############################################
ants-2.1.0/Scripts/waitForPBSQJobs.pl-132- # Use of backticks rather than system permits a ctrl+c to work
ants-2.1.0/Scripts/waitForPBSQJobs.pl:133: `sleep $delay`;
ants-2.1.0/Scripts/waitForPBSQJobs.pl:134: $qstatOutput = `qstat -u $user`;
ants-2.1.0/Scripts/waitForPBSQJobs.pl-135- @qstatLines = split("\n", $qstatOutput);
##############################################
ants-2.1.0/Scripts/waitForSGEQJobs.pl-35-
ants-2.1.0/Scripts/waitForSGEQJobs.pl:36:my $qstatOutput = `qstat -u $user`;
ants-2.1.0/Scripts/waitForSGEQJobs.pl-37-
##############################################
ants-2.1.0/Scripts/waitForSGEQJobs.pl-114- # Use of backticks rather than system permits a ctrl+c to work
ants-2.1.0/Scripts/waitForSGEQJobs.pl:115: `sleep $delay`;
ants-2.1.0/Scripts/waitForSGEQJobs.pl:116: $qstatOutput = `qstat -u $user`;
ants-2.1.0/Scripts/waitForSGEQJobs.pl-117- @qstatLines = split("\n", $qstatOutput);
##############################################
ants-2.1.0/Scripts/waitForXGridJobs.pl-57-#$statline = 0;
ants-2.1.0/Scripts/waitForXGridJobs.pl:58:#@result = `xgrid $xgridflags -job attributes -id $jobIDs[i]`;
ants-2.1.0/Scripts/waitForXGridJobs.pl-59-#for ($i=0; $i<scalar(@result); $i++) {
##############################################
ants-2.1.0/Scripts/waitForXGridJobs.pl-80- # Get the status of this ID
ants-2.1.0/Scripts/waitForXGridJobs.pl:81: @result = `xgrid $xgridflags -job attributes -id $job`;
ants-2.1.0/Scripts/waitForXGridJobs.pl-82- $statline=0;
##############################################
ants-2.1.0/Scripts/waitForXGridJobs.pl-117- print " ($timestamp) Still waiting for $jobsIncomplete jobs - sleeping $delay\n\n";
ants-2.1.0/Scripts/waitForXGridJobs.pl:118: `sleep $delay`;
ants-2.1.0/Scripts/waitForXGridJobs.pl-119- }
##############################################
ants-2.1.0/Scripts/warpimages.pl-44- system $waitcmd;
ants-2.1.0/Scripts/warpimages.pl:45: $output = `$waitcmd`;
ants-2.1.0/Scripts/warpimages.pl-46-
##############################################
ants-2.1.0/Scripts/weightedaverage.sh-5-count=9
ants-2.1.0/Scripts/weightedaverage.sh:6:for x in `ls -tr $1 `
ants-2.1.0/Scripts/weightedaverage.sh-7-do
ants-2.1.0/Scripts/weightedaverage.sh:8: count=`expr $count + 1` # Increment the counter
ants-2.1.0/Scripts/weightedaverage.sh-9- echo " count is $count and file is $x at it $i "
##############################################
ants-2.1.0/SuperBuild.cmake-14-#-----------------------------------------------------------------------------
ants-2.1.0/SuperBuild.cmake:15:include(${CMAKE_CURRENT_SOURCE_DIR}/Common.cmake)
ants-2.1.0/SuperBuild.cmake-16-
##############################################
ants-2.1.0/antsRegistrationCLP/CMakeLists.txt-2-find_package(SlicerExecutionModel REQUIRED GenerateCLP)
ants-2.1.0/antsRegistrationCLP/CMakeLists.txt:3:include(${GenerateCLP_USE_FILE})
ants-2.1.0/antsRegistrationCLP/CMakeLists.txt-4-
##############################################
ants-2.1.0/.pc/deb_local-data.patch/CMake/ANTSExternalData.cmake-1-get_filename_component(_ITKExternalData_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
ants-2.1.0/.pc/deb_local-data.patch/CMake/ANTSExternalData.cmake:2:include(${_ITKExternalData_DIR}/ExternalData.cmake)
ants-2.1.0/.pc/deb_local-data.patch/CMake/ANTSExternalData.cmake-3-